Environmental and Human Pathogenic Microorganisms

  • Philippe Lebaron
  • Benoit Cournoyer
  • Karine Lemarchand
  • Sylvie Nazaret
  • Pierre Servais
Chapter

Abstract

As the study of interactions between pathogenic microorganisms and their environment is part of microbial ecology, this chapter reviews the different types of human pathogens found in the environment, the different types of fecal indicators used in water quality monitoring, the biotic and abiotic factors affecting the survival and the infectivity of pathogenic microorganisms during their transportation in the environment, and the methods presently available to detect rare microorganisms in environmental samples. This chapter exclusively focuses on human pathogens.

Keywords

Pathogens Wastewater treatment plant Dissemination Antibiotic resistance Environmental reservoirs Toxins Sanitary microbiology Biological pollution 

Abbreviations

AIDS

Acquired immunodeficiency syndrome

BOD

Biological oxygen demand

CSO

Combined sewer overflow

HAV

Hepatitis A virus

HEV

Hepatitis E virus

GI

Genomic islands

ID50

The dose of an infectious organism required to produce infection in 50 % of the experimental subjects

Ig

Immunoglobulin

IS

Insertion sequence

LPS

Lipopolysaccharide

MID

Minimal infectious dose

OECD

Organization for Economic Co-operation and Development

PAI

Pathogenicity islands

SS

Suspended solids

IPCC

Intergovernmental Panel on Climate Change

VNC

Viable but non-culturable

WWTP

Wastewater treatment plant

References

  1. Aendekerk S, Ghysels B, Cornelis P, Baysse C (2002) Characterization of a new efflux pump, MexGHI-OpmD, from Pseudomonas aeruginosa that confers resistance to vanadium. Microbiology 148:2371–2381PubMedGoogle Scholar
  2. Alonso A, Rojo F, Martinez JL (1999) Environmental and clinical isolates of Pseudomonas aeruginosa show pathogenic and biodegradative properties irrespective of their origin. Environ Microbiol 1:421–430PubMedCrossRefGoogle Scholar
  3. Behets J, Declerck P, Delaedt Y, Verelst L, Ollevier F (2007) Survey for the presence of specific free-living amoebae in cooling waters from Belgian power plants. Parasitol Res 100:1249–1256PubMedCrossRefGoogle Scholar
  4. Berg G, Eberl L, Hartmann A (2005a) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7:1673–1685PubMedCrossRefGoogle Scholar
  5. Berg J, Tom-Petersen A, Nybroe O (2005b) Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field. Lett Appl Microbiol 40:146–151PubMedCrossRefGoogle Scholar
  6. Berg J, Thorsen MK, Holm PE, Jensen J, Nybroe O, Brandt KK (2010) Cu exposure under field conditions coselects for antibiotic resistance as determined by a novel cultivation-independent bacterial community tolerance assay. Environ Sci Technol 44:8724–8728PubMedCrossRefGoogle Scholar
  7. Briand E, Yépremian C, Humbert JF, Quiblier C (2008) Comparative studies on the fitness of microcystin-producing and non-producing Planktothrix agardhii strains cultivated under different environmental conditions. Environ Microbiol 10:3337–3348PubMedCrossRefGoogle Scholar
  8. Briand E, Escoffier N, Straub C, Sabart M, Quiblier C, Humbert JF (2009) Spatiotemporal changes in the genetic diversity of a bloom-forming Microcystis aeruginosa (cyanobacteria) population. ISME J 3:419–429PubMedCrossRefGoogle Scholar
  9. Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155:376–386PubMedCrossRefGoogle Scholar
  10. Chen J, Novick RP (2009) Phage-mediated intergeneric transfer of toxin genes. Science 323:139–141PubMedCrossRefGoogle Scholar
  11. Colwell R, Grimes DJ (2000) Nonculturable microorganisms in the environment. ASM Press, Washington, DCCrossRefGoogle Scholar
  12. Davies-Colley RJ, Donnison AM, Speed DJ (1997) Sunlight wavelengths inactivating faecal indicator microorganisms in waste stabilization ponds. Water Sci Technol 35:219–225CrossRefGoogle Scholar
  13. Davies-Colley RJ, Donnison AM, Speed DJ, Ross CM, Nagels JW (1999) Inactivation of faecal indicator microorganisms in waste stabilisation ponds: interactions of environmental factors with sunlight. Water Res 53:1220–1230CrossRefGoogle Scholar
  14. D’Costa VM et al (2011) Antibiotic resistance is ancient. Nature 477:457–461PubMedCrossRefGoogle Scholar
  15. Delecluse P (2008) The origin of climate changes. Rev Sci Tech Off Int Epiz 27:309–317Google Scholar
  16. Desnues B, Cuny C, Grégori G, Dukan S, Aguilaniu H, Nyström T (2003) Differential oxidative damage and expression of stress defense regulons in culturable and non-culturable Escherichia coli cells. EMBO Rep 4(4):400–404PubMedCentralPubMedCrossRefGoogle Scholar
  17. Downing JA, Watson SB, McCauley E (2001) Predicting Cyanobacteria dominance in lakes. Can J Fish Aquat Sci 58:1905–1908CrossRefGoogle Scholar
  18. Dukan S, Nyström T (1998) Bacterial senescence: stasis results in increased and differential oxidation of cytoplasmic proteins leading to developmental induction of the heat shock regulon. Genes Dev 12:3431–3441PubMedCentralPubMedCrossRefGoogle Scholar
  19. Edberg SC, Le Clerc H, Robertson J (2000) Escherichia coli: the best biological drinking water indicator for public health protection. J Appl Microbiol 88:1068–1168Google Scholar
  20. Fajardo A, Martínez JL (2008) Antibiotic as signals that trigger specific bacterial responses. Curr Opin Microbiol 11:161–167PubMedCrossRefGoogle Scholar
  21. Fewtrell L, Bartram J (2001) Water quality: guidelines, standards and health. World Health Organization water series. IWA Publishing, LondonGoogle Scholar
  22. Fields BS, Benson RF, Besser RE (2002) Legionella and Legionnaires’ disease: 25 years of investigation. Clin Microbiol Rev 15:506–526PubMedCentralPubMedCrossRefGoogle Scholar
  23. Frangeul L et al (2008) Highly plastic genome of Microcystis aeruginosa PCC7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 9:274PubMedCentralPubMedCrossRefGoogle Scholar
  24. Gagliardi JV, Karns JS (2002) Persistence of Escherichia coli O157:H7 in soil and on plant roots. Environ Microbiol 4:89–96PubMedCrossRefGoogle Scholar
  25. Garcia Armisen T, Servais P (2004) Enumeration of viable E. coli in rivers and wastewaters by fluorescent in situ hybridization. J Microbiol Methods 58:269–279PubMedCrossRefGoogle Scholar
  26. Garcia Armisen T, Servais P (2007) Respective contributions of point and non point sources of E. coli and Enterococci in a large urbanised watershed (the Seine river, France). J Environ Manage 82(4):512–518PubMedCrossRefGoogle Scholar
  27. 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 35:275–283PubMedCrossRefGoogle Scholar
  28. Garrett L (1996) The return of infectious disease. Foreign Aff 75:66–79CrossRefGoogle Scholar
  29. George I, Crop P, Servais P (2002) Fecal coliforms removal in wastewater treatment plants studied by plate counts and enzymatic methods. Water Res 36:2607–2617PubMedCrossRefGoogle Scholar
  30. Guan TY, Holley RA (2003) Pathogen survival in swine manure environments and transmission of human enteric illness–a review. J Environ Qual 32:383–392PubMedCrossRefGoogle Scholar
  31. Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679PubMedCrossRefGoogle Scholar
  32. Heuer H, Smalla K (2007) Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ Microbiol 9:657–666PubMedCrossRefGoogle Scholar
  33. Heuer H, Schmitt H, Smalla K (2011) Antibiotic resistance gene spread due to manure application on agricultural fields. Curr Opin Microbiol 14:236–243PubMedCrossRefGoogle Scholar
  34. Hijnen WAM, Beerendonck EF, Medema GJ (2006) Inactivation credit of UV radiation for viruses, bacteria and protozoan (oo)cysts in water: a review. Water Res 40:3–22PubMedCrossRefGoogle Scholar
  35. Huysman F, Verstraete W, Brookes PC (1994) Effect of manuring practices and increased copper concentrations on soil microbial populations. Soil Biol Biochem 26:103–110CrossRefGoogle Scholar
  36. Kaestli M et al (2007) Sensitive and specific molecular detection of Burkholderia pseudomallei, the causative agent of melioidosis, in the soil of Tropical Northern Australia. Appl Environ Microbiol 73:6891–6897PubMedCentralPubMedCrossRefGoogle Scholar
  37. Karaolis DK, Somara S, Maneval DR Jr, Johnson JA, Kaper JB (1999) A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 399:375–379PubMedCrossRefGoogle Scholar
  38. Karci A, Balcioğlu IA (2009) Investigation of the tetracycline, sulfonamide, and fluoroquinolone antimicrobial compounds in animal manure and agricultural soils in Turkey. Sci Total Environ 407:4652–4664PubMedCrossRefGoogle Scholar
  39. Kidd SE, Chow Y, Mak S, Bach PJ, Chen H, Hingston AO, Kronstad JW, Bartlett KH (2007) Characterization of environmental sources of the human and animal pathogen, Cryptococcus gattii, in British Columbia, Canada, and Pacific Northwest USA. Appl Environ Microbiol 73:1433–1443PubMedCentralPubMedCrossRefGoogle Scholar
  40. Knapp S, Hacker J, Jarchau T, Goebel W (1986) Large, unstable inserts in the chromosome affect virulence properties of uropathogenic Escherichia coli O6 strain 536. J Bacteriol 168:22–30PubMedCentralPubMedGoogle Scholar
  41. Knapp CW, Zhang W, Sturm BS, Graham DW (2010) Differential fate of erythromycin and beta-lactam resistance genes from swine lagoon waste under different aquatic conditions. Environ Pollut 158:1506–1512PubMedCrossRefGoogle Scholar
  42. Koelle K, Pascual M, Yunus M (2005) Pathogen adaptation to seasonal forcing and climate change. Proc R Soc B 272:971–977PubMedCentralPubMedCrossRefGoogle Scholar
  43. Kogure K, Simidu U, Taga N (1979) A tentative direct microscopic method for counting living marine bacteria. Can J Microbiol 25:415–420PubMedCrossRefGoogle Scholar
  44. Kong KF, Schneper L, Mathee K (2010) Beta-lactam antibiotics: from antibiosis to resistance and bacteriology. APMIS 118:1–36PubMedCentralPubMedCrossRefGoogle Scholar
  45. Kulasekara BR, Kulasekara HD, Wolfgang MC, Stevens L, Frank DW, Lory S (2006) Acquisition and evolution of the exoU locus in Pseudomonas aeruginosa. J Bacteriol 188:4037–4050PubMedCentralPubMedCrossRefGoogle Scholar
  46. Kummerer J (2003) The significance of antibiotics in the environment. J Antimicrob Chemother 1:5–7CrossRefGoogle Scholar
  47. Kuske CR, Barns SM, Grow CC, Merrill L, Dunbar J (2006) Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes. J Forensic Sci 51:548–558PubMedCrossRefGoogle Scholar
  48. Lavenir R, Jocktane D, Laurent F, Nazaret S, Cournoyer B (2007) Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target. J Microbiol Methods 70:20–29PubMedCrossRefGoogle Scholar
  49. Lebaron P, Henry A, Lepeuple A-S, Pena G, Servais P (2005) An operational method for real-time monitoring of E. coli in bathing waters. Mar Polluut Bull 50:652–659CrossRefGoogle Scholar
  50. Levy SB, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10:S122–S129PubMedCrossRefGoogle Scholar
  51. Lin H, Xu B, Chen Y, Wang W (2009) Legionella pollution in cooling tower water of air-conditioning systems in Shanghai, China. J Appl Microbiol 106:606–612PubMedCrossRefGoogle Scholar
  52. Lindgren E, Gustafson R (2001) Tick-borne encephalitis in Sweden and climate change. Lancet 358:16–18PubMedCrossRefGoogle Scholar
  53. Lindsay JA, Ruzin A, Ross HF, Kurepina N, Novick RP (1998) The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Mol Microbiol 29:527–543PubMedCrossRefGoogle Scholar
  54. Marsalek J, Rochfort Q (2004) Urban wet-weather flows: sources of fecal contamination impacting on recreational waters and threatening drinking-water sources. J Toxicol Environ Health Part A Curr Issues 67(20–22):1765–1777CrossRefGoogle Scholar
  55. Martinez JL, Fajardo A, Garmendia L, Hernandez A, Linares JF, Martínez-Solano L, Sánchez MB (2009) A global view of antibiotic resistance. FEMS Microbiol Rev 33:44–65PubMedCrossRefGoogle Scholar
  56. Mesaros N et al (2007) Pseudomonas aeruginosa: resistance and therapeutic options at the turn of the new millennium. Clin Microbiol Infect 13:560–578PubMedCrossRefGoogle Scholar
  57. Mukherjee A, Cho S, Scheftel J, Jawahir S, Smith K, Diez-Gonzalez F (2006) Soil survival of Escherichia coli O157: H7 acquired by a child from garden soil recently fertilized with cattle manure. J Appl Microbiol 101:429–436PubMedCrossRefGoogle Scholar
  58. Norman RS, Moeller P, Mc Donald TJ, Morris PJ (2004) Effect of pyocyanin on a crude-oil-degrading microbial community. Appl Environ Microbiol 70:4004–4011PubMedCentralPubMedCrossRefGoogle Scholar
  59. Ogden LD, Fenlon DR, Vinten AJ, Lewis D (2001) The fate of Escherichia coli O157 in soil and its potential to contaminate drinking water. Int J Food Microbiol 66:111–117PubMedCrossRefGoogle Scholar
  60. Oliver JD (2010) Recent findings on the viable but nonculturable sate in pathogenic bacteria. FEMS Microbiol Rev 34:415–425PubMedGoogle Scholar
  61. Ouattara KN, Passerat J, Servais P (2011) Faecal contamination of water and sediment in the rivers of the Scheldt drainage network. Environ Monit Assess 183:243–257PubMedCrossRefGoogle Scholar
  62. Paerl HW, Huisman J (2009) Climate change: a catalyst for global expansion of harmful cyanobacterial blooms. Environ Microbiol 1:27–37CrossRefGoogle Scholar
  63. Palasatien S, Lertsirivorakul R, Royros P, Wongratanacheevin S, Sermswan RW (2008) Soil physicochemical properties related to the presence of Burkholderia pseudomallei. Trans R Soc Trop Med Hyg 1:S5–S9CrossRefGoogle Scholar
  64. Pelandakis M, Pernin P (2002) Use of multiplex PCR and PCR restriction enzyme analysis for detection and exploration of the variability in the free-living amoeba Naegleria in the environment. Appl Environ Microbiol 68:2061–2065PubMedCentralPubMedCrossRefGoogle Scholar
  65. Perron K, Caille O, Rossier C, Van Delden C, Dumas JL, Köhler T (2004) CzcR-CzcS, a two-component system involved in heavy metal and carbapenem resistance in Pseudomonas aeruginosa. J Biol Chem 279:8761–8768PubMedCrossRefGoogle Scholar
  66. Philippot L (2005) Denitrification in pathogenic bacteria: for better or worst ? Trends Microbiol 13:191–192PubMedCrossRefGoogle Scholar
  67. Qiu X, Gurkar AU, Lory S (2006) Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 103:19830–19835PubMedCentralPubMedCrossRefGoogle Scholar
  68. Ready PD (2008) Leishmaniasis emergence and climate change. Rev Sci Tech Off Int Epiz 27:399–412Google Scholar
  69. Ready D, Pratten J, Mordan N, Watts E, Wilson M (2007) The effect of amalgam exposure on mercury- and antibiotic-resistant bacteria. Int J Antimicrob Agents 30:34–39PubMedCrossRefGoogle Scholar
  70. Rose JB, Farrah SR, Harwood VJ, Levine AD, Lukasik J, Menendez P, Scott T (2004) Reduction of pathogens, indicators bacteria and alternative indicators by wastewater treatment and reclamation processes. WERF final report. IWA Publishing, LondonGoogle Scholar
  71. Salazar-Lindo E, Seas C, Gutierrez D (2008) ENSO and cholera in South America: what can we learn about it from the 1991 cholera outbreak? Int J Environ Health 2:30–36CrossRefGoogle Scholar
  72. Savichtcheva O, Okabe S (2006) Alternative indicators of fecal pollution: relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring and future application perspectives. Water Res 40:2463–2476PubMedCrossRefGoogle Scholar
  73. Schwaiger K, Harms K, Hölzel C, Meyer K, Karl M, Bauer J (2009) Tetracycline in liquid manure selects for co-occurrence of the resistance genes tet(M) and tet(L) in Enterococcus faecalis. Vet Microbiol 139:386–392PubMedCrossRefGoogle Scholar
  74. Servais P, Garcia Armisen T, Lepeuple AS, Lebaron P (2005) An early warning method to detect fecal contamination of river waters. Ann Microbiol 55:67–72Google Scholar
  75. Servais P, Garcia-Armisen T, George I, Billen G (2007) Fecal bacteria in the rivers of the Seine drainage network: source, fate and modeling. Sci Tot Environ 375:152–167CrossRefGoogle Scholar
  76. Simango C (2006) Prevalence of Clostridium difficile in the environment in a rural community in Zimbabwe. Trans R Soc Trop Med Hyg 100:1146–1150PubMedCrossRefGoogle Scholar
  77. Solomon EB, Yaron S, Matthews KR (2002) Transmission of Escherichia coli O157:H7 from contaminated manure and irrigation water to lettuce plant tissue and its subsequent internalization. Appl Environ Microbiol 68:397–400PubMedCentralPubMedCrossRefGoogle Scholar
  78. Stepanauskas R, Glenn TC, Jagoe CH, Tuckfield RC, Lindell AH, King CJ, McArthur JV (2006) Coselection for microbial resistance to metals and antibiotics in freshwater microcosms. Environ Microbiol 8:1510–1514PubMedCrossRefGoogle Scholar
  79. Taubes G (2008) The bacteria fight back. Science 321:356–361PubMedCrossRefGoogle Scholar
  80. Tello A, Austin B, Telfer TC (2012) Selective pressure of antibiotic pollution on bacteria of importance to public health. Environ Health Perspect 120:1100–1106PubMedCentralPubMedCrossRefGoogle Scholar
  81. Thompson JR, Marcelino LA, Polz MF (2010) Diversity, sources, and detection of human bacterial pathogens in the marine environment. In: Belkin S, Colwell RR (eds) Oceans and health, pathogens in the marine environment. Springer, New York, pp 29–68Google Scholar
  82. Vally H, Whittle A, Cameron S, Dowse GK, Watson T (2004) Outbreak of Aeromonas hydrophila wound infections associated with mud football. Clin Infect Dis 38:1084–1089PubMedCrossRefGoogle Scholar
  83. Vedler E, Vahter M, Heinaru A (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol 186:7161–7174PubMedCentralPubMedCrossRefGoogle Scholar
  84. Von der Weid I, Marques JM, Cunha CD, Lippi RK, Dos Santos SC, Rosado AS, Lins U, Seldin L (2007) Identification and biodegradation potential of a novel strain of Dietzia cinnamea isolated from a petroleum-contaminated tropical soil. Syst Appl Microbiol 4:331–339CrossRefGoogle Scholar
  85. Wery N, Bru-Adan V, Minervini C, Delgénes JP, Garrelly L, Godon JJ (2008) Dynamics of Legionella spp. and bacterial populations during the proliferation of L. pneumophila in a cooling tower facility. Appl Environ Microbiol 74:3030–3037PubMedCentralPubMedCrossRefGoogle Scholar
  86. Wright GD (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 5:175–186PubMedCrossRefGoogle Scholar
  87. Xu HS, Roberts NC, Adams LB, West PA, Siebeling RJ, Huq A, Huq MI, Rahman R, Colwell RR (1982) An indirect fluorescent antibody staining procedure for detection of Vibrio cholerae serovar 01 cells in aquatic environmental samples. J Microbiol Methods 2:221–231CrossRefGoogle Scholar
  88. You Y, Rankin SC, Aceto HW, Benson CE, Toth JD, Dou Z (2006) Survival of Salmonella enterica serovar Newport in manure and manure-amended soils. Appl Environ Microbiol 72:5777–5783PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Philippe Lebaron
    • 1
  • Benoit Cournoyer
    • 3
  • Karine Lemarchand
    • 2
  • Sylvie Nazaret
    • 3
  • Pierre Servais
    • 4
  1. 1.Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM)Sorbonne Universités, UPMC Univ Paris 06, USR CNRS 3579Banyuls-sur-MerFrance
  2. 2.Laboratoire de Bactériologie marine et Écotoxicologie microbienneInstitut des sciences de la mer de RimouskiRimouskiCanada
  3. 3.Microbial Ecology CenterUMR CNRS 5557 / USC INRA 1364, Université Lyon 1VilleurbanneFrance
  4. 4.Laboratoire d’Écologie des Systèmes Aquatiques (ESA)Université Libre de BruxellesBruxellesBelgium

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