1887

Chapter 3.3.2 : Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.3.2-1.gif /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.3.2-2.gif

Abstract:

Soils receive inputs of human pathogenic and indicator bacteria through land application of animal manures or sewage sludge, and inputs by wildlife. Soil is an extremely heterogeneous substrate and contains meso- and macrofauna that may be reservoirs for bacteria of human health concern. The ability to detect and quantify bacteria of human health concern is important in risk assessments and in evaluating the efficacy of agricultural soil management practices that are protective of crop quality and protective of adjacent water resources. The present chapter describes the distribution of selected Gram-positive and Gram-negative bacteria in soils. Methods for detecting and quantifying soilborne bacteria including extraction, enrichment using immunomagnetic capture, culturing, molecular detection and deep sequencing of metagenomic DNA to detect pathogens are overviewed. Methods for strain phenotypic and genotypic characterization are presented, as well as how comparison with clinical isolates can inform the potential for human health risk.

Citation: Boschiroli M, Falkinham J, Favre-Bonté S, Nazaret S, Piveteau P, Sadowsky M, Byappanahalli M, Delaquis P, Hartmann A. 2016. Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria, p 3.3.2-1-3.3.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.3.2
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555818821.ch3.3.2
1. Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, Herrera-Estrella L, Olmedo G. 2010. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 11:332.[PubMed][CrossRef]
2. Dierick K, Van Coillie E, Swiecicka I, Meyfroidt G, Devlieger H, Meulemans A, Hoedemaekers G, Fourie L, Heyndrickx M, Mahillon J. 2005. Fatal family outbreak of Bacillus cereus-associated food poisoning. J Clin Microbiol 43:42774279.[PubMed][CrossRef]
3. Guillet C, Join-Lambert O, Le Monnier A, Leclercq A, Mechaï F, Mamzer-Bruneel MF, Bielecka MK, Scortti M, Disson O, Berche P, Vazquez-Boland J, Lortholary O, Lecuit M. 2010. Human listeriosis caused by Listeria ivanovii. Emerg Infect Dis 16:136138.[PubMed][CrossRef]
4. Donnelly CW. 2001. Listeria monocytogenes: a continuing challenge. Nutr Rev 59:183194.[PubMed][CrossRef]
5. Byappanahalli MN, Ishii S,. 2011. Environmental sources of fecal bacteria, p 93110. In Sadowsky MJ,, Whitman RL (eds), The Fecal Bacteria. ASM Press, Washington, DC.
6. Ferguson D, Signoretto C,. 2011. Environmental persistence and naturalization of fecal indicator organisms, p 379397. In Hagedorn C,, Blanch AR,, Harwood VJ (eds), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer, New York.
7. Whitman R, Nevers M, Przybyla-Kelly K, Byappanahalli MN,. 2011. Physical and biological factors influencing environmental sources of fecal indicator bacteria in surface water, p 111134. In Sadowsky MJ,, Whitman RL (eds), The Fecal Bacteria. ASM Press, Washington, DC.
8. Howell JM, Coyne MS, Cornelius P. 1995. Fecal bacteria in agricultural waters of the Bluegrass Region of Kentucky. J Environ Qual 24:411419.[CrossRef]
9. Stephenson GR, Street LV. 1978. Bacterial variations in streams from a Southwest Idaho rangeland watershed. J Environ Qual 7:150156.[CrossRef]
10. Grange JM. 1996. The biology of the genus Mycobacterium. J Appl Bacteriol 81:S1S9.
11. Primm TP, Lucero CA, Falkinham JO. 2004. Health impacts of environmental mycobacteria. Clin Microbiol Rev 17:98106.[PubMed][CrossRef]
12. Brooke JS. 2012. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev 25:241.[PubMed][CrossRef]
13. Jones RN, Sader HS, Beach ML. 2003. Contemporary in vitro spectrum of activity summary for antimicrobial agents tested against 18569 strains non-fermentative Gram-negative bacilli isolated in the SENTRY Antimicrobial Surveillance Program (1997–2001). Int J Antimicrob Agents 22:551556.[PubMed][CrossRef]
14. Razvi S, Quittell L, Sewall A, Quinton H, Marshall B, Saiman L. 2009. Respiratory microbiology of patients with cystic fibrosis in the United States, 1995 to 2005. Chest 136:15541560.[PubMed][CrossRef]
15. Sanchez MB, Hernandez A, Martinez JL. 2009. Stenotrophomonas maltophilia drug resistance. Future Microbiol 4:655660.[PubMed][CrossRef]
16. Smith LD. 1978. Occurrence of Clostridium botulinum and Clostridium tetani in soil of United-States. Health Lab Sci 15:7480.[PubMed]
17. Cook TM, Protheroe RT, Handel JM. 2001. Tetanus: a review of the literature. Br J Anaesth 87:477487.[PubMed][CrossRef]
18. Huss HH. 1980. Distribution of Clostridium botulinum. Appl Environ Microbiol 39:764769.[PubMed]
19. Smith GR, Young AM. 1980. Clostridium botulinum in British soil. J Hyg (Lond) 85:271274.[CrossRef]
20. Notermans S, Dufrenne J, Oosterom J. 1981. Persistence of Clostridium botulinum Type-B on a cattle farm after an outbreak of botulism. Appl Environ Microbiol 41:179183.[PubMed]
21. Matches JR, Liston J, Curran D. 1974. Clostridium perfringens in the environment. Appl Microbiol 28:655660.[PubMed]
22. Li JH, Sayeed S, McClane BA. 2007. Prevalence of enterotoxigenic Clostridium perfringens isolates in Pittsburgh (Pennsylvania) area soils and home kitchens. Appl Environ Microbiol 73:72187224.[CrossRef]
23. Lahti P, Lindstrom M, Somervuo P, Heikinheimo A, Korkeala H. 2012. Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens Type A. PLoS One 7:e46162.[CrossRef]
24. Arnesen LPS, Fagerlund A, Granum PE. 2008. From soil to gut: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Rev 32:579606.[CrossRef]
25. Vilain S, Luo Y, Hildreth MB, Brozel VS. 2006. Analysis of the life cycle of the soil saprophyte Bacillus cereus in liquid soil extract and in soil. Appl Environ Microbiol 72:49704977.[PubMed][CrossRef]
26. Saunders BD, Wideman M. 2007. Ecology of Listeria species and L. monocytogenes in the natural environment. Food Sci Technol 161:2154.
27. Freitag NE, Port GC, Miner MD. 2009. Listeria monocytogenes—from saprophyte to intracellular pathogen. Nat Rev Microbiol 7:623628.[PubMed][CrossRef]
28. Gorski L, Duhe JM, Flaherty D. 2011. The Sigma B operon is a determinant of fitness for a Listeria monocytogenes serotype 4b strain in soil. Foodborne Pathog Dis 8:699704.[PubMed][CrossRef]
29. Welshimer HJ. 1960. Survival of Listeria monocytogenes in soil. J Bacteriol 80:316320.[PubMed]
30. Weis J, Seeliger HPR. 1975. Incidence of Listeria monocytogenes in nature. Appl Microbiol 30:2932.[PubMed]
31. Dowe MJ, Jackson ED, Mori JG, Bell CR. 1997. Listeria monocytogenes survival in soil and incidence in agricultural soils. J Food Prot 60:12011207.
32. Fenlon DR, Wilson J, Donachie W. 1996. The incidence and level of Listeria monocytogenes contamination of food sources at primary production and initial processing. J Appl Bacteriol 81:641650.[PubMed]
33. Garrec N, Picard Bonnaud F, Pourcher AM. 2003. Occurrence of Listeria sp. and L. monocytogenes in sewage sludge used for land application: effect of dewatering, liming and storage in tank on survival of Listeria species. FEMS Immunol Med Microbiol 35:275283.[PubMed][CrossRef]
34. Welshimer HJ. 1968. Isolation of Listeria monocytogenes from vegetation. J Bacteriol 95:300303.[PubMed]
35. Welshimer HJ, Donker-Voet J. 1971. Listeria monocytogenes in nature. Appl Microbiol 21:516519.[PubMed]
36. Lyautey E, Hartmann A, Pagotto F, Tyler K, Lapen DR, Wilkes G, Piveteau P, Rieu A, Robertson WJ, Medeiros DT, Edge TA, Gannon V, Topp E. 2007. Characteristics and frequency of detection of fecal Listeria monocytogenes shed by livestock, wildlife, and humans. Can J Microbiol 53:11581167.[PubMed][CrossRef]
37. Lyautey E, Lapen DR, Wilkes G, McCleary K, Pagotto F, Tyler K, Hartmann A, Piveteau P, Rieu A, Robertson WJ, Medeiros DT, Edge TA, Gannon V, Topp E. 2007. Distribution and characteristics of Listeria monocytogenes isolates from surface waters of the South Nation River watershed, Ontario, Canada. Appl Environ Microbiol 73:54015410.[PubMed][CrossRef]
38. Guan TY, Holley RA. 2003. Pathogen survival in swine manure environments and transmission of human enteric illness: a review. J Environ Qual 32:383392.[PubMed][CrossRef]
39. Al-Ghazali MR, Al-Azawi SK. 1990. Listeria monocytogenes contamination of crops grown on soil treated with sewage sludge cake. J Appl Bacteriol 69:642647.[PubMed]
40. Paillard D, Dubois V, Thiebaut R, Nathier F, Hoogland E, Caumette P, Quentin C. 2005. Occurrence of Listeria spp. in effluents of French urban wastewater treatment plants. Appl Environ Microbiol 71:75627566.[PubMed][CrossRef]
41. Byappanahalli MN, Roll BM, Fujioka RS. 2012. Evidence for occurrence, persistence, and growth potential of Escherichia coli and enterococci in Hawaii's soil environments. Microbes Environ 27:164170.[PubMed][CrossRef]
42. Goto DK, Yan T. 2011. Effects of land uses on fecal indicator bacteria in the water and soil of a tropical watershed. Microbes Environ 26:254260.[PubMed][CrossRef]
43. Fujioka R, Sian-Denton C, Borja M, Castro J, Morphew K. 1999. Soil: the environmental source of Escherichia coli and enterococci in Guam's streams. J Appl Microbiol 85:83S89S.[CrossRef]
44. Hardina CM, Fujioka RS. 1991. Soil—the environmental source of Escherichia coli and enterococci in Hawaii streams. Environ Toxicol Water Qual 6:185195.[CrossRef]
45. Hazen TC. 1988. Fecal coliforms as indicators in tropical waters—a review. Tox Assess 3:461477.[CrossRef]
46. Lasalde C, Rodriguez R, Toranzos GA, Smith HH. 2005. Heterogeneity of uidA gene in environmental Escherichia coli populations. J Water Health 3:297304.[PubMed]
47. Desmarais TR, Solo-Gabriele HM, Palmer CJ. 2002. Influence of soil on fecal indicator organisms in a tidally influenced subtropical environment. Appl Environ Microbiol 68:11651172.[PubMed][CrossRef]
48. Solo-Gabriele HM, Wolfert MA, Desmarais TR, Palmer CJ. 2000. Sources of Escherichia coli in a coastal subtropical environment. Appl Environ Microbiol 66:230237.[PubMed][CrossRef]
49. Brennan FP, Abram F, Chinalia FA, Richards KG, O'Flaherty V. 2010. Characterization of environmentally persistent Escherichia coli isolates leached from an Irish soil. Appl Environ Microbiol 76:21752180.[PubMed][CrossRef]
50. Byappanahalli MN, Shively DA, Nevers MB, Sadowsky MJ, Whitman RL. 2003. Growth and survival of Escherichia coli and enterococci populations in the macro-alga Cladophora (Chlorophyta). FEMS Microbiol Ecol 46:203211.[PubMed][CrossRef]
51. Ishii S, Yan T, Shively DA, Byappanahalli MN, Whitman RL, Sadowsky MJ. 2006. Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan. Appl Environ Microbiol 72:45454553.[PubMed][CrossRef]
52. Bergholz PW, Noar JD, Buckley DH. 2011. Environmental patterns are imposed on the population structure of Escherichia coli after fecal deposition. Appl Environ Microbiol 77:211219.[PubMed][CrossRef]
53. Byappanahalli MN, Whitman RL, Shively DA, Sadowsky MJ, Ishii S. 2006. Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environ Microbiol 8:504513.[PubMed][CrossRef]
54. Whitman RL, Nevers MB, Byappanahalli MN. 2006. Examination of the watershed-wide distribution of Escherichia coli along Southern Lake Michigan: an integrated approach. Appl Environ Microbiol 72:73017310.[PubMed][CrossRef]
55. Byappanahalli MN, Fujioka RS. 2004. Indigenous soil bacteria and low moisture may limit but allow faecal bacteria to multiply and become a minor population in tropical soils. Water Sci Technol 50:2732.[PubMed]
56. Chandler DS, Craven JA. 1980. Relationship of soil-moisture to survival of Escherichia coli and Salmonella typhimurium in soils. Aust J Agric Res 31:547555.[CrossRef]
57. Hunter C, McDonald A. 1991. The occurrence of coliform bacteria in the surface soils of 2 catchment areas in the Yorkshire Dales. J Inst Water Environ Manag 5:534538.[CrossRef]
58. Fujioka RS, Byappanahalli MN, 2001. Microbial ecology controls the establishment of fecal bacteria in tropical soil environment, p. 273283. In Matsuo TH,, Takizawa K,, Satoh SH (eds), Advances in Water and Wastewater Treatment Technology: Molecular Technology, Nutrient Removal, Sludge Reduction and Environmental Health. Elsevier, Amsterdam.
59. Walker TS, Bais HP, Grotewold E, Vivanco JM. 2003. Root exudation and rhizosphere biology. Plant Physiol 132:4451.[PubMed][CrossRef]
60. Biet F, Boschiroli ML, Thorel MF, Guilloteau LA. 2005. Zoonotic aspects of Mycobacterium bovis and Mycobacterium avium-intracellulare complex (MAC). Vet Res 36:411436.[PubMed][CrossRef]
61. Kazda J, Pavlik I, Falkinham JO, Hruska K. 2009. The Ecology of Mycobacteria: Impact on Animal and Human Health. Springer, Rotterdam.
62. Young JS, Gormley E, Wellington EM. 2005. Molecular detection of Mycobacterium bovis and Mycobacterium bovis BCG (Pasteur) in soil. Appl Environ Microbiol 71:19461952.[PubMed][CrossRef]
63. Sweeney FP, Courtenay O, Ul-Hassan A, Hibberd V, Reilly LA, Wellington EMH. 2006. Immunomagnetic recovery of Mycobacterium bovis from naturally infected environmental samples. Lett Appl Microbiol 43:364369.[PubMed][CrossRef]
64. Travis ER, Gaze WH, Pontiroli A, Sweeney FP, Porter D, Mason S, Keeling MJC, Jones RM, Sawyer J, Aranaz A, Rizaldos EC, Cork J, Delahay RJ, Wilson GJ, Hewinson RG, Courtenay O, Wellington EMH. 2011. An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of Mycobacterium bovis. PLoS One 6:e27369.[PubMed][CrossRef]
65. Brooks RW, Parker BC, Gruft H, Falkinham JO. 1984. Epidemiology of infection by nontuberculous mycobacteria.5. Numbers in eastern-United-States soils and correlation with soil characteristics. Am Rev Respir Dis 130:630633.[PubMed]
66. Radomski N, Thibault VC, Karoui C, de Cruz K, Cochard T, Gutiérrez C, Supply P, Biet F, Boschiroli ML. 2010. Determination of genotypic diversity of Mycobacterium avium subspecies from human and animal origins by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat and IS1311 restriction fragment length polymorphism typing methods. J Clin Microbiol 48:10261034.[PubMed][CrossRef]
67. Pickup RW, Rhodes G, Arnott S, Sidi-Boumedine K, Bull TJ, Weightman A, Hurley M, Hermon-Taylor J. 2005. Mycobacterium avium subsp paratuberculosis in the catchment area and water of the river Taff in South Wales, United Kingdom, and its potential relationship to clustering of Crohn's disease cases in the city of Cardiff. Appl Environ Microbiol 71:21302139.[PubMed][CrossRef]
68. De Groote MA, Pace NR, Fulton K, Falkinham JO. 2006. Relationships between Mycobacterium isolates from patients with pulmonary mycobacterial infection and potting soils. Appl Environ Microbiol 72:76027606.[PubMed][CrossRef]
69. Juhnke ME, des Jardin E. 1989. Selective medium for isolation of Xanthomonas maltophilia from soil and rhizosphere environments. Appl Environ Microbiol 55:747750.[PubMed]
70. Romano G, Stampi S, Zanetti F, De Luca G, Tonelli E. 1997. Occurrence of gram-negative bacteria in drinking water undergoing softening treatment. Int J Hyg Environ Health 200:152162.
71. Dungan RS, Yates SR, Frankenberger WT. 2003. Transformations of selenate and selenite by Stenotrophomonas maltophilia isolated from a seleniferous agricultural drainage pond sediment. Environ Microbiol 5:287295.[PubMed][CrossRef]
72. Berg G, Eberl L, Hartmann A. 2005. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7:16731685.[PubMed][CrossRef]
73. Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, Berg G, van der Lelie D, Dow JM. 2009. The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat Rev Microbiol 7:514525.[PubMed][CrossRef]
74. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Slinkina NN, Mikhailov VV. 2008. Occurrence and antagonistic potential of Stenotrophomonas strains isolated from deep-sea invertebrates. Arch Microbiol 189:337344.[PubMed][CrossRef]
75. Flores MR, Ordoñez OF, Maldonado MJ, Farías ME. 2009. Isolation of UV-B resistant bacteria from two high altitude Andean lakes (4,400 m) with saline and non saline conditions. J Gen Appl Microbiol 55:447458.[PubMed][CrossRef]
76. Matyar F, Kaya A, Dinçer S. 2008. Antibacterial agents and heavy metal resistance in Gram-negative bacteria isolated from seawater, shrimp and sediment in Iskenderun Bay, Turkey. Sci Total Environ 407:279285.[PubMed][CrossRef]
77. Brennan PJ, Nikaido H. 1995. The envelope of mycobacteria. Ann Rev Biochem 64:2963.[PubMed][CrossRef]
78. Brooks RW, George KL, Parker BC, Falkinham JO, Gruft H. 1984. Recovery and survival of nontuberculous mycobacteria under various growth and decontamination conditions. Can J Microbiol 30:11121117.[PubMed][CrossRef]
79. Thorel MF, Moreau R, Charvin M, Ebiou D. 1991. Release of mycobacteria from natural environment by enzymes. C R Séances Soc Biol Fil 185:331337.[PubMed]
80. Strahl ED, Gillaspy GE, Falkinham JO. 2001. Fluorescent acid-fast microscopy for measuring phagocytosis of Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum by Tetrahymena pyriformis and their intracellular growth. Appl Environ Microbiol 67:44324439.[PubMed][CrossRef]
81. Cirillo JD, Falkow S, Tompkins LS, Bermudez LE. 1997. Interaction of Mycobacterium avium with environmental amoebae enhances virulence. Infect Immun 65:37593767.[PubMed]
82. Mazurek GH, Reddy V, Murphy D, Ansari T. 1996. Detection of Mycobacterium tuberculosis in cerebrospinal fluid following immunomagnetic enrichment. J Clin Microbiol 34:450453.[PubMed]
83. Sweeney FP, Courtenay O, Hibberd V, Hewinson RG, Reilly LA, Gaze WH, Wellington EMH. 2007. Environmental monitoring of Mycobacterium bovis in badger feces and badger sett soil by real-time PCR, as confirmed by immunofluorescence, immunocapture, and cultivation. Appl Environ Microbiol 73:74717473.[PubMed][CrossRef]
84. Voidarou C, Bezirtzoglou E, Alexopoulos A, Plessas S, Stefanis C, Papadopoulos I, Vavias S, Stavropoulou E, Fotou K, Tzora A, Skoufos I. 2011. Occurrence of Clostridium perfringens from different cultivated soils. Anaerobe 17:320324.[PubMed][CrossRef]
85. Lúquez C, Bianco MI, de Jong LIT, Sagua MD, Arenas GN, Ciccarelli AS, Fernández RA. 2005. Distribution of botulinum toxin-producing clostridia in soils of Argentina. Appl Environ Microbiol 71:41374139.[PubMed][CrossRef]
86. Sanada I, Nishida S. 1965. Isolation of Clostridium tetani from soil. J Bacteriol 89:626629.[PubMed]
87. Dragon DC, Rennie RP, Elkin BT. 2001. Detection of anthrax spores in endemic regions of northern Canada. J Appl Microbiol 91:435441.[PubMed][CrossRef]
88. Sauders BD, Overdevest J, Fortes E, Windham K, Schukken Y, Lembo A, Wiedmann M. 2012. Diversity of Listeria species in urban and natural environments. Appl Environ Microbiol 78:44204433.[PubMed][CrossRef]
89. Hitchins AD. 2003. Detection and enumeration of Listeria monocytogenes in foods. In U.S. Food and Drug Administration, Bacteriological Analytical Manual. Washington, DC.
90. USDA, Service FSaI. 2013. Isolation and identification of Listeria monocytogenes from red meat, poultry, egg and environmental samples. In USDA Food and Safety and Inspection Service, Microbiology Laboratory Guidebook, http://www.fsis.usda.gov/wps/portal/fsis/topics/science/laboratories-and-procedures/guidebooks-and-methods/microbiology-laboratory-guidebook/microbiology-laboratory-guidebook.
91. Atlas R. 2010. Handbook of Microbiological Media, 4th ed. ASM Press and CRC Press, Washington, DC.
92. Park SH, Ryu S, Kang DH. 2011. Improved selective and differential medium for isolation of Escherichia coli O157:H7. J Clin Microbiol 49:405408.[PubMed][CrossRef]
93. Santamaria J, Toranzos GA. 2003. Enteric pathogens and soil: a short review. Int Microbiol 6:59.[PubMed]
94. Zuberer DA,. 1994. Recovery and enumeration of viable bacteria, p 119144. In Weaver RW (ed), Methods of Soil Analysis, Part 2. Microbiological and Biochemical Properties. Soil Society of America, Madison, WI.
95. Pepper IL, Gerba CP,. 2009. Cultural methods, p 173189. In Maier RM,, Pepper IL,, Gerba CP (eds), Environmental Microbiology, 2nd ed. Academic Press, San Diego, CA.
96. Archuleta RJ, Hoppes PY, Primm TP. 2005. Mycobacterium avium, enters a state of metabolic dormancy in response to starvation. Tuberculosis 85:147158.[PubMed][CrossRef]
97. Kerr KG, Denton M, Todd N, Corps CM, Kumari P, Hawkey PM. 1996. A new selective differential medium for isolation of Stenotrophomonas maltophilia. Eur J Clin Microbiol Infect Dis 15:607610.[PubMed][CrossRef]
98. Pinot C, Deredjian A, Nazaret S, Brothier E, Cournoyer B, Segonds C, Favre-Bonté S. 2011. Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure. J Appl Microbiol 111:11851193.[PubMed][CrossRef]
99. Foddai A, Elliott CT, Grant IR. 2010. Maximizing capture efficiency and specificity of magnetic separation for Mycobacterium avium subsp. paratuberculosis cells. Appl Environ Microbiol 76:75507558.[PubMed][CrossRef]
100. Stewart LD, McNair J, McCallan L, Thompson S, Kulakov LA, Grant IR. 2012. Production and evaluation of antibodies and phage display-derived peptide ligands for immunomagnetic separation of Mycobacterium bovis. J Clin Microbiol 50:15981605.[PubMed][CrossRef]
101. Radomski N, Lucas FS, Moilleron R, Cambau E, Haenn S, Moulin L. 2010. Development of a real-time qPCR method for detection and enumeration of Mycobacterium spp. in surface water. Appl Environ Microbiol 76:73487351.[PubMed][CrossRef]
102. Colinon C, Deredjian A, Hien E, Brothier E, Bouziri L, Cournoyer B, Hartmann A, Henry S, Jolivet C, Ranjard L, Nazaret S. 2013. Detection and enumeration of Pseudomonas aeruginosa in soil and manure assessed by an ecfX qPCR assay. J Appl Microbiol 114:17341749.[PubMed][CrossRef]
103. Locatelli A, Depret G, Jolivet C, Henry S, Dequiedt S, Piveteau P, Hartmann A. 2013. Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods. J Microbiol Meth 93:242250.[CrossRef]
104. Ranjard L, Lejon DPH, Mougel C, Schehrer L, Merdinoglu D, Chaussod R. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5:11111120.[PubMed][CrossRef]
105. Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G. 2001. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67:43974397.[CrossRef]
106. Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Laval K, Lebeau T, Lemanceau P, Leyval C, Lindstrom K, Pandard P, Romero E, Sarr A, Schloter M, Simonet P, Smalla K, Wilke BM, Martin-Laurent F. 2011. Inter-laboratory evaluation of the ISO standard 11063 “Soil quality—method to directly extract DNA from soil samples.” J Microbiol Meth 84:454460.[CrossRef]
107. Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, Pace NR. 2009. Opportunistic pathogens enriched in showerhead biofilms. Proc Natl, Acad Sci USA 106:1639316398.[CrossRef]
108. Wilton S, Cousins D. 1992. Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube. PCR Meth Appl 1:269273.[CrossRef]
109. Wang H, Edwards M, Falkinham JO, Pruden A. 2012. Molecular survey of the occurrence of Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa, and amoeba hosts in two chloraminated drinking water distribution systems. Appl Environ Microbiol 78:62856294.[PubMed][CrossRef]
110. Tortoli E, Rindi L, Garcia MJ, Chiaradonna P, Dei R, Garzelli C, Kroppenstedt RM, Lari N, Mattei R, Mariottini A, Mazzarelli G, Murcia MI, Nanetti A, Piccoli P, Scarparo C. 2004. Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov. Int J Syst Evol Microbiol 54:12771285.[PubMed][CrossRef]
111. Tortoli E. 2003. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16:319354.[PubMed][CrossRef]
112. Kirschner RA, Parker BC, Falkinham JO. 1992. Epidemiology of infection by nontuberculous mycobacteria—Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in acid, brown-water swamps of the Southeastern United-States and their association with environmental variables. Am Rev Respir Dis 145:271275.[PubMed][CrossRef]
113. Iivanainen EK, Martikainen PJ, Raisanen ML, Katila ML. 1997. Mycobacteria in boreal coniferous forest soils. FEMS Microbiol Ecol 23:325332.[CrossRef]
114. Jadhav S, Bhave M, Palombo EA. 2012. Methods used for the detection and subtyping of Listeria monocytogenes. J Microbiol Meth 88:327341.[CrossRef]
115. Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:26842691.[PubMed][CrossRef]
116. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.[PubMed][CrossRef]
117. Lindstrom ES, Kamst-Van Agterveld MP, Zwart G. 2005. Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. Appl Environ Microbiol 71:82018206.[PubMed][CrossRef]
118. Mueller-Spitz SR, Goetz GW, McLellan SL. 2009. Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan. FEMS Microbiol Ecol 67:511522.[PubMed][CrossRef]
119. Schmidt TM, Delong EF, Pace NR. 1991. Analysis of a marine picoplankton community by 16 s ribosomal-RNA gene cloning and sequencing. J Bacteriol 173:43714378.[PubMed]
120. von Wintzingerode F, Gobel UB, Stackebrandt E. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213229.[PubMed][CrossRef]
121. Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. 2009. Microbial community structure in the North Pacific ocean. ISME J 3:13741386.[PubMed][CrossRef]
122. Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449456.[PubMed][CrossRef]
123. Zwart G, Crump BC, Agterveld MPKV, Hagen F, Han SK. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microbiol Ecol 28:141155.[CrossRef]
124. Ishii S, Segawa T, Okabe S. 2013. Simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative PCR. Appl Environ Microbiol 79:28912898.[PubMed][CrossRef]
125. Luo CW, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. 2011. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci USA 108:72007205.[PubMed][CrossRef]
126. Ishii S, Ksoll WB, Hicks RE, Sadowsky MJ. 2006. Presence and growth of naturalized Escherichia coli in temperate soils from lake superior watersheds. Appl Environ Microbiol 72:612621.[PubMed][CrossRef]
127. Ishii S, Hansen DL, Hicks RE, Sadowsky MJ. 2007. Beach sand and sediments are temporal sinks and sources of Escherichia coli in lake superior. Environ Sci Technol 41:22032209.[PubMed][CrossRef]
128. Byappanahalli MN, Whitman RL, Shively DA, Ferguson J, Ishii S, Sadowsky MJ. 2007. Population structure of Cladophora-borne Escherichia coli in nearshore water of Lake Michigan. Water Res 41:36493654.[PubMed][CrossRef]
129. Badgley BD, Ferguson J, Vanden Heuvel A, Kleinheinz GT, McDermott CM, Sandrin TR, Kinzelman J, Junion EA, Byappanahalli MN, Whitman RL, Sadowsky MJ. 2011. Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan. Water Res 45:721731.[PubMed][CrossRef]
130. Muller T, Ulrich A, Ott EM, Muller M. 2001. Identification of plant-associated enterococci. J Appl Microbiol 91:268278.[PubMed][CrossRef]
131. Ott EM, Muller T, Muller M, Franz CMAP, Ulrich A, Gabel M, Seyfarth W. 2001. Population dynamics and antagonistic potential of enterococci colonizing the phyllosphere of grasses. J Appl Microbiol 91:5466.[PubMed][CrossRef]
132. Hartz A, Cuvelier M, Nowosielski K, Bonilla TD, Green M, Esiobu N, McCorquodale DS, Rogerson A. 2008. Survival potential of Escherichia coli and enterococci in subtropical beach sand: implications for water quality managers. J Environ Qual 37:898905.[PubMed][CrossRef]
133. Yamahara KM, Walters SP, Boehm AB. 2009. Growth of enterococci in unaltered, unseeded beach sands subjected to tidal wetting. Appl Environ Microbiol 75:15171524.[PubMed][CrossRef]
134. Byappanahalli MN, Sawdey R, Ishii S, Shively DA, Ferguson JA, Whitman RL, Sadowsky MJ. 2009. Seasonal stability of Cladophora-associated Salmonella in Lake Michigan watersheds. Water Res 43:806814.[PubMed][CrossRef]
135. Gubelit YI, Vainshtein MB. 2011. Growth of enterobacteria on algal mats in the eastern part of the Gulf of Finland. Inland Water Biol 4:132136.[CrossRef]
136. Baess I. 1974. Isolation and purification of desoxyribonucleic acid from mycobacteria. Acta Pathol Microbiol Scand B Microbiol Immunol 82:780784.[PubMed]
137. Telenti A, Marchesi F, Balz M, Bally F, Bottger EC, Bodmer T. 1993. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31:175178.[PubMed]
138. Steingrube VA, Gibson JL, Brown BA, Zhang YS, Wilson RW, Rajagopalan M, Wallace RJ. 1995. PCR amplification and restriction endonuclease analysis of a 65-kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria. J Clin Microbiol 33:16861686.
139. Arbeit RD, Slutsky A, Barber TW, Maslow JN, Niemczyk S, Falkinham JO, Oconnor GT, Vonreyn CF. 1993. Genetic diversity among strains of Mycobacterium avium causing monoclonal and polyclonal bacteremia in patients with AIDS. J Infect Dis 167:13841390.[PubMed][CrossRef]
140. van Soolingen D, Bauer J, Ritacco V, Leão SC, Pavlik I, Vincent V, Rastogi N, Gori A, Bodmer T, Garzelli C, Garcia MJ. 1998. IS1245 restriction fragment length polymorphism typing of Mycobacterium avium isolates: proposal for standardization. J Clin Microbiol 36:30513054.[PubMed]
141. Cangelosi GA, Freeman RJ, Lewis KN, Livingston-Rosanoff D, Shah KS, Milan SJ, Goldberg SV. 2004. Evaluation of a high-throughput repetitive-sequence-based PCR system for DNA fingerprinting of Mycobacterium tuberculosis and Mycobacterium avium complex strains. J Clin Microbiol 42:26852693.[PubMed][CrossRef]
142. Dauchy FA, Degrange S, Charron A, Dupon M, Xin Y, Bebear C, Maugein J. 2010. Variable-number tandem-repeat markers for typing Mycobacterium intracellulare strains isolated in humans. BMC Microbiol 10:93.[PubMed][CrossRef]
143. Ichikawa K, Yagi T, Inagaki T, Moriyama M, Nakagawa T, Uchiya K, Nikai T, Ogawa K. 2010. Molecular typing of Mycobacterium intracellulare using multilocus variable-number of tandem-repeat analysis: identification of loci and analysis of clinical isolates. Microbiology 156:496504.[PubMed][CrossRef]
144. Skuce RA, Brittain D, Hughes MS, Neill SD. 1996. Differentiation of Mycobacterium bovis isolates from animals by DNA typing. J Clin Microbiol 34:24692474.[PubMed]
145. Collins DM, Cavaignac S, deLisle GW. 1997. Use of four DNA insertion sequences to characterize strains of the Mycobacterium avium complex isolated from animals. Mol Cell Probes 11:373380.[PubMed][CrossRef]
146. Nadon CA, Woodward DL, Young C, Rodgers EG, Wiedmann M. 2001. Correlations between molecular subtyping and serotyping of Listeria monocytogenes. J Clin Microbiol 39:27042707.[PubMed][CrossRef]
147. Ragon M, Wirth T, Hollandt F, Lavenir R, Lecuit M, Le Monnier A, Brisse S. 2008. A new perspective on Listeria monocytogenes evolution. PLoS Pathog 4:e1000146.[PubMed][CrossRef]
148. Chenal-Francisque V, Lopez J, Cantinelli T, Caro V, Tran C, Leclercq A, Lecuit M, Brisse S. 2011. Worldwide distribution of major clones of Listeria monocytogenes. Emerg Infect Dis 17:11101112.[PubMed][CrossRef]
149. Ward TJ, Gorski L, Borucki MK, Mandrell RE, Hutchins J, Pupedis K. 2004. Intraspecific phylogeny and lineage group identification based on the prfA virulence gene cluster of Listeria monocytogenes. J Bacteriol 186:49945002.[PubMed][CrossRef]
150. Wiedmann M, Bruce JL, Keating C, Johnson AE, McDonough PL, Batt CA. 1997. Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential. Infect Immun 65:27072716.[PubMed]
151. Gray MJ, Zadoks RN, Fortes ED, Dogan B, Cai S, Chen YH, Scott VN, Gombas DE, Boor KJ, Wiedmann M. 2004. Listeria monocytogenes isolates from foods and humans form distinct but overlapping populations. Appl Environ Microbiol 70:58335841.[PubMed][CrossRef]
152. Gudmundsdottir KB, Aalbaek B, Sigurdarson S, Gunnarsson E. 2004. The diversity of Listeria monocytogenes strains from 10 Icelandic sheep farms. J Appl Microbiol 96:913921.[PubMed][CrossRef]
153. Nightingale KK, Schukken YH, Nightingale CR, Fortes ED, Ho AJ, Her Z, Grohn YT, McDonough PL, Wiedmann M. 2004. Ecology and transmission of Listeria monocytogenes infecting ruminants and in the farm environment. Appl Environ Microbiol 70:44584467.[PubMed][CrossRef]
154. Sauders BD, Durak MZ, Fortes E, Windham K, Schukken Y, Lembo AJJr., Akey B, Nightingale KK, Wiedmann M. 2006. Molecular characterization of Listeria monocytogenes from natural and urban environments. J Food Prot 69:93105.[PubMed]

Tables

Generic image for table
TABLE 1

Examples of methods used for the recovery of human pathogens from soils

Citation: Boschiroli M, Falkinham J, Favre-Bonté S, Nazaret S, Piveteau P, Sadowsky M, Byappanahalli M, Delaquis P, Hartmann A. 2016. Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria, p 3.3.2-1-3.3.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.3.2
Generic image for table
TABLE 2

Summary of DNA-based methods for identification/typing of

Citation: Boschiroli M, Falkinham J, Favre-Bonté S, Nazaret S, Piveteau P, Sadowsky M, Byappanahalli M, Delaquis P, Hartmann A. 2016. Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria, p 3.3.2-1-3.3.2-12. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.3.2

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error