QPCR standard operating procedure for measuring microorganisms in dust from dwellings in large cohort studies

Science of the Total Environment

Volumn 466-467, Issue , 2014, Pages 716-724

  Scherer, Emeline ^a,b   Rocchi, Steffi ^a   Reboux, Gabriel ^a,b   Vandentorren, Stéphanie ^c   Roussel, Sandrine ^a   Vacheyrou, Mallory ^a,b   Raherison, Chantal ^d,e   Millon, Laurence ^a,b  

^a UNIVERSITÉ DE FRANCHE COMTÉ   (France)

^b UNIVERSITY HOSPITAL OF BESANÇON   (France)

^c INSTITUT DE VEILLE SANITAIRE   (France)

^d University Hospital   (France)

^e UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

Chronic exposure; Dust mites; Environmental bacteria; Environmental fungi; Indoor microorganisms; Wipes

Indexed keywords

CHRONIC EXPOSURE; DUST MITE; INFLAMMATORY PROCESS; OPERATIONAL PROCEDURES; PENICILLIUM CHRYSOGENUM; QUANTIFICATION LIMIT; STANDARD OPERATING PROCEDURES; WIPES;

DUST; ELECTROSTATICS; FUNGI; HOUSING; MICROBIOLOGY; POLYMERASE CHAIN REACTION;

BACTERIA;

FUNGAL DNA; ALLERGEN; BACTERIAL DNA; DUST;

CONCENTRATION (COMPOSITION); DNA; DUST; INDOOR AIR; MICROBIAL ACTIVITY; MICROORGANISM; NUMERICAL MODEL; POLYMERASE CHAIN REACTION;

ACTINOBACTERIA; ANALYTICAL EQUIPMENT; ARTICLE; BACTERIUM; COHORT ANALYSIS; CONTROLLED STUDY; DERMATOPHAGOIDES PTERONYSSINUS; DNA EXTRACTION; DUST; ELECTROSTATIC DUST FALL COLLECTOR; ENTEROBACTERIACEAE; ENVIRONMENTAL EXPOSURE; FUNGUS SPORE; HOUSEHOLD; LIMIT OF DETECTION; MEASUREMENT REPEATABILITY; MICROBIAL CONTAMINATION; MICROORGANISM DETECTION; MITE; MOULD; MYCOBACTERIUM; NONHUMAN; PENICILLIUM CHRYSOGENUM; PILOT STUDY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SAMPLING; SENSITIVITY AND SPECIFICITY; ANALYSIS; ANIMAL; CHILD; ENVIRONMENTAL MONITORING; EVALUATION STUDY; FUNGUS; GENETICS; HOUSING; HUMAN; INDOOR AIR POLLUTION; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; PROCEDURES; PYROGLYPHIDAE;

AIR POLLUTION, INDOOR; ALLERGENS; ANIMALS; BACTERIA; CHILD; DNA, BACTERIAL; DNA, FUNGAL; DUST; ENVIRONMENTAL MONITORING; FUNGI; HOUSING; HUMANS; MOLECULAR SEQUENCE DATA; PILOT PROJECTS; POLYMERASE CHAIN REACTION; PYROGLYPHIDAE;

EID: 84882963776     PISSN: 00489697     EISSN: 18791026     Source Type: Journal    
DOI: 10.1016/j.scitotenv.2013.07.054     Document Type: Article

References (49)

1. Arshad S.H. Does exposure to indoor allergens contribute to the development of asthma and allergy?. Curr Allergy Asthma Rep 2010, 10:49-55.
2. Asher M.I., Montefort S., Bjorksten B., Lai C.K., Strachan D.P., Weiland S.K., et al. Worldwide time trends in the prevalence of symptoms of asthma, allergic rhinoconjunctivitis, and eczema in childhood: ISAAC Phases One and Three repeat multicountry cross-sectional surveys. Lancet 2006, 368:733-743.
3. Bouillard L., Michel O., Dramaix M., Devleeschouwer M. Bacterial contamination of indoor air, surfaces, and settled dust, and related dust endotoxin concentrations in healthy office buildings. Ann Agric Environ Med 2005, 12:187-192.
4. Braun-Fährlander C., Gassner M., Grize L., Neu U., Sennhauser F.H., Varonier H.S., et al. Prevalence of hay fever and allergic sensitization in farmer's children and their peers living in the same rural community. SCARPOL team. Swiss study on childhood allergy and respiratory symptoms with respect to air pollution. Clin Exp Allergy 1999, 29:28-34.
5. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55:611-622.
6. Chew G.L., Rogers C., Burge H.A., Muilenberg M.L., Gold D.R. Dustborne and airborne fungal propagules represent a different spectrum of fungi with differing relations to home characteristics. Allergy 2003, 58:13-20.
7. Dawson D.J. Potential pathogens among strains of mycobacteria isolated from house-dusts. Med J Aust 1971, 1:679-681.
8. Development Core Team 2012, R: A Language and Environment for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0].
9. Eder W., Ege M.J., von Mutius E. The asthma epidemic. N Engl J Med 2006, 355:2226-2235.
10. Frankel M., Timm M., Hansen E.W., Madsen A.M. Comparison of sampling methods for the assessment of indoor microbial exposure. Indoor Air 2012, 22:405-414.
11. Gehring U., Heinrich J., Hoek G., Giovannangelo M., Nordling E., Bellander T., et al. Bacteria and mould components in house dust and children's allergic sensitisation. Eur Respir J 2007, 29:1144-1153.
12. Gibbons J.G., Rokas A. The function and evolution of the Aspergillus genome. Trends Microbiol 2013, 21:14-22.
13. Harrison P.T. Creature comforts-living with mites and moulds. Clin Exp Allergy 1999, 29:148-149.
14. Haugland R.A., Vesper S.J., Wymer L.J. Quantitative measurement of Stachybotrys chartarum conidia using real time detection of PCR products with the TaqMan(™) fluorogenic probe system. Mol Cell Probes 1999, 13:329-340.
15. Haugland R.A., Brinkman N., Vesper S.J. Evaluation of rapid DNA extraction methods for the quantitative detection of fungi using real-time PCR analysis. J Microbiol Methods 2002, 50:319-323.
16. Haugland R.A., Varma M., Wymer L.J., Vesper S.J. Quantitative PCR analysis of selected Aspergillus, Penicillium and Paecilomyces species. Syst Appl Microbiol 2004, 27:198-210.
17. Hirvonen M.R., Huttunen K., Roponen M. Bacterial strains from moldy buildings are highly potent inducers of inflammatory and cytotoxic effects. Indoor Air 2005, 15(Suppl. 9):65-70.
18. Hospodsky D., Yamamoto N., Peccia J. Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi. Appl Environ Microbiol 2010, 76:7004-7012.
19. Huttunen K., Pelkonen J., Nielsen K.F., Nuutinen U., Jussila J., Hirvonen M.R. Synergistic interaction in simultaneous exposure to Streptomyces californicus and Stachybotrys chartarum. Environ Health Perspect 2004, 112:659-665.
20. Kaarakainen P., Rintala H., Vepsalainen A., Hyvarinen A., Nevalainen A., Meklin T. Microbial content of house dust samples determined with qPCR. Sci Total Environ 2009, 407:4673-4680.
21. Keswani J., Kashon M.L., Chen B.T. Evaluation of interference to conventional and real-time PCR for detection and quantification of fungi in dust. J Environ Monit 2005, 7:311-318.
22. Kuhn D.M., Ghannoum M.A. Indoor mold, toxigenic fungi, and Stachybotrys chartarum: infectious disease perspective. Clin Microbiol Rev 2003, 16:144-172.
23. Lignell U., Meklin T., Rintala H., Hyvarinen A., Vepsalainen A., Pekkanen J., et al. Evaluation of quantitative PCR and culture methods for detection of house dust fungi and streptomycetes in relation to moisture damage of the house. Lett Appl Microbiol 2008, 47:303-308.
24. Meklin T., Haugland R.A., Reponen T., Varma M., Lummus Z., Bernstein D., et al. Quantitative PCR analysis of house dust can reveal abnormal mold conditions. J Environ Monit 2004, 6:615-620.
25. Normand A.C., Vacheyrou M., Sudre B., Heederik D.J., Piarroux R. Assessment of dust sampling methods for the study of cultivable-microorganism exposure in stables. Appl Environ Microbiol 2009, 75:7617-7623.
26. Noss I., Wouters I.M., Visser M., Heederik D.J., Thorne P.S., Brunekreef B., et al. Evaluation of a low-cost electrostatic dust fall collector for indoor air endotoxin exposure assessment. Appl Environ Microbiol 2008, 74:5621-5627.
27. Obihara C.C., Bollen C.W., Beyers N., Kimpen J.L. Mycobacterial infection and atopy in childhood: a systematic review. Pediatr Allergy Immunol 2007, 18:551-559.
28. Ownby D.R., Peterson E.L., Williams L.K., Zoratti E.M., Wegienka G.R., Woodcroft K.J., et al. Variation of dust endotoxin concentrations by location and time within homes of young children. Pediatr Allergy Immunol 2010, 21:533-540.
29. Reboux G., Bellanger A.P., Roussel S., Grenouillet F., Sornin S., Piarroux R., et al. Indoor mold concentration in Eastern France. Indoor Air 2009, 19:446-453.
30. Reponen T., Vesper S., Levin L., Johansson E., Ryan P., Burkle J., et al. High environmental relative moldiness index during infancy as a predictor of asthma at 7years of age. Ann Allergy Asthma Immunol 2011, 107:120-126.
31. Rintala H., Nevalainen A. Quantitative measurement of streptomycetes using real-time PCR. J Environ Monit 2006, 8:745-749.
32. Rintala H., Hyvarinen A., Paulin L., Nevalainen A. Detection of streptomycetes in house dust-comparison of culture and PCR methods. Indoor Air 2004, 14:112-119.
33. Roe J.D., Haugland R.A., Vesper S.J., Wymer L.J. Quantification of Stachybotrys chartarum conidia in indoor dust using real time, fluorescent probe-based detection of PCR products. J Expo Anal Environ Epidemiol 2001, 11:12-20.
34. Roussel S., Reboux G., Naegele A., Martinez J., Vacheyrou M., Scherer E., et al. Detecting and quantifying mites in domestic dust: a novel application for real-time PCR. Environ Int 2013, 55:20-24.
35. Sen K., Asher D.M. Multiplex PCR for detection of Enterobacteriaceae in blood. Transfusion 2001, 41:1356-1364.
36. Sergey A., Grinshpun M., Buttner M.P., Willeke K. Sampling for airborne microorganisms. Manual of environmental microbiology 2007, 939-953. American Society of Microbiology, Washington DC. C.J. Hurst, R.L. Crawford, J.L. Garland, D.A. Lipson, A.L. Mills, L.D. Stetzenbach (Eds.).
37. Tischer C.G., Heinrich J. Exposure assessment of residential mould, fungi and microbial components in relation to children's health: achievements and challenges. Int J Hyg Environ Health 2013, 216(2):109-114.
38. Torvinen E., Meklin T., Torkko P., Suomalainen S., Reiman M., Katila M.L., et al. Mycobacteria and fungi in moisture-damaged building materials. Appl Environ Microbiol 2006, 72:6822-6824.
39. Torvinen E., Torkko P., Rintala A.N. Real-time PCR detection of environmental mycobacteria in house dust. J Microbiol Methods 2010, 82:78-84.
40. Vallance G., McSharry C., Wood S., Thomson N.C. House dust mite control measures in the treatment of asthma. Ther Clin Risk Manag 2006, 2:347-354.
41. Van Asselt L. Interactions between domestic mites and fungi. Indoor Built Environ 1999, 216-220.
42. Vandentorren S., Bois C., Pirus C., Sarter H., Salines G., Leridon H. Rationales, design and recruitment for the ELFE longitudinal study. BMC Pediatr 2009, 9:58.
43. Vesper S. Traditional mould analysis compared to a DNA-based method of mould analysis. Crit Rev Microbiol 2011, 37:15-24.
44. Vesper S., McKinstry C., Haugland R., Wymer L., Bradham K., Ashley P., et al. Development of an environmental relative moldiness index for US homes. J Occup Environ Med 2007, 49:829-833.
45. Vesper S., McKinstry C., Haugland R., Neas L., Hudgens E., Heidenfelder B., et al. Higher Environmental Relative Moldiness Index (ERMIsm) values measured in Detroit homes of severely asthmatic children. Sci Total Environ 2008, 394:192-196.
46. von Mutius E. Allergies, infections and the hygiene hypothesis-the epidemiological evidence. Immunobiology 2007, 212:433-439.
47. von Mutius E. Asthma and allergies in rural areas of Europe. Proc Am Thorac Soc 2007, 4:212-216.
48. Yamamoto N., Shendell D.G., Peccia J. Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air 2011, 21:521-530.
49. Zeng Q.Y., Westermark S.O., Rasmuson-Lestander A., Wang X.R. Detection and quantification of Cladosporium in aerosols by real-time PCR. J Environ Monit 2006, 8:153-160.