Molecular source tracking of bioaerosols in the quarantined katrina flood zone

Aerosol Science and Technology

Volumn 44, Issue 3, 2010, Pages 230-239

  De Evgrafov, Mari Rodríguez ^a   Walker, Jeffery J ^b   Pace, Norman R ^b   Hernandez, Mark T ^a  

^a University of Colorado   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AEROSOLIZATION; AIRBORNE MICROBE; BIOAEROSOLS; BROAD SPECTRUM; DNA SEQUENCING ANALYSIS; EMERGENCY RESPONSE; ENGINEERING OPERATION; ENGINEERING WORKS; FLOOD ZONES; KATRINA; MICRO DROPLETS; MOLECULAR SOURCES; NEW ORLEANS; OUTDOOR BIOAEROSOL; PATHOGENIC MICROORGANISMS; PATHOGENIC SPECIES; SAMPLING CAMPAIGNS; SKIN INFECTION; WATER SAMPLES;

BIOCHEMICAL OXYGEN DEMAND; ECOLOGY; HURRICANES; MOLECULAR BIOLOGY; OXYGEN; POLLUTION; PUMPS;

MICROORGANISMS;

DNA; RIBOSOME RNA;

AERATION; AEROSOL; AIR SAMPLING; AIRBORNE MICROORGANISM; ARTICLE; BIOAEROSOL; CONTROLLED STUDY; DNA SEQUENCE; ECOLOGICAL NICHE; FLOODING; GENETIC ANALYSIS; HURRICANE; INFECTION CONTROL; MICROBIAL POPULATION DYNAMICS; MICROSCOPY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; UNITED STATES; WATER SAMPLING;

EID: 77949613892     PISSN: 02786826     EISSN: 15217388     Source Type: Journal    
DOI: 10.1080/02786820903543046     Document Type: Article

References (60)

1. Acinas, S. G., Sarma-Rupavtarm, R., Klepac-Ceraj, V., and Polz, M. F. (2005). PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample. Appl. Environ. Microbiol. 71:8966-8969.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic Local Alignment Search Tool. J. Mol. Biol. 215:403-410.
3. Alvarez, A. J., Buttner,M. P., and Stetzenbach, L.D. (1995). PCR for Bioaerosol Monitoring-Sensitivity and Environmental Interference. Appl. Environ. Microbiol. 61:3639-3644.
4. Amann, R. I., Ludwig,W., and Schleifer, K. H. (1995). Phylogenetic Identification and In-Situ Detection of Individual Microbial-Cells without Cultivation. Microbiol. Rev. 59:143-169.
5. Angenent, L. T., Kelley, S. T., St Amand, A., Pace, N. R., and Hernandez, M. T. (2005). Molecular Identification of Potential Pathogens in Water and Air of a Hospital Therapy Pool. Proc. Natl. Acad. Sci. USA 102:4860-4865.
6. Baertsch, C., Paez-Rubio, T., Viau, E., and Peccia, J. (2007). Source Tracking Aerosols Released from Land-Applied Class B Biosolids During High-Wind Events. Appl. Environ. Microbiol. 73:4522-4531.
7. Becker, S., Boger, P., Oehlmann, R., and Ernst, A. (2000). PCR Bias in Ecological Analysis: A Case Study for Quantitative Taq Nuclease Assays in Analyses of Microbial Communities. Appl. Environ. Microbiol. 66:4945-4953.
8. Blanchard, D., and Syzdek, L. (1970).Mechanism for theWater-to-Air Transfer and Concentration of Bacteria. Science 170:626-628.
9. Blanchard, D., and Syzdek, L. (1971). Bubbles and Water-To Air Transfer of Bacteria Bull. Amer. Meteorol. Soc. 52:1136.
10. Blanchard, D. C., and Syzdek, L. D. (1972). Concentration of Bacteria in Jet Drops from Bursting Bubbles. J. Geophys. Res. 77:5087-5099.
11. Blanchard, D. C., and Syzdek, L. D. (1982). Water-to-Air Transfer and Enrichment of Bacteria in Drops from Bursting Bubbles. Appl. Environ. Microbiol. 43:1001-1005.
12. Brodie, E. L., DeSantis, T. Z., Parker, J. P. M., Zubietta, I. X., Piceno, Y. M., and Andersen, G. L. (2007). Urban Aerosols Harbor Diverse and Dynamic Bacterial Populations. Proc. Natl. Acad. Sci. USA 104:299-304.
13. Burge, H. (1990). Bioaerosols-Prevalence and Health-Effects in the Indoor Environment. J. Allergy and Clinical Immunology 86:687-701.
14. CDC (2005). Infectious Disease and Dermatologic Conditions in Evacuees and Rescue Workers After Hurricane Katrina-Multiple States, August-September, 2005. JAMA 294:2158-2160.
15. Chao, A. (1984). Nonparametric-Estimation of the Number of Classes in a Population. Scan. J. Statistics 11:265-270.
16. Currier, M., King, D. S.,Wofford, M. R., Daniel, B. J., and deShazo, R. (2006). A Katrina Experience: Lessons Learned. Amer. J. Medicine 119:986-992.
17. DeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., and et al. (2006). NAST: A Multiple Sequence Alignment Server for Comparative Analysis of 16S rRNA Genes. Nucleic Acids Res. 34:W394-W399.
18. Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-Calling of Automated Sequencer Traces Using phred. I. Accuracy Assessment. Genome Research 8:175-185.
19. Fabian,M. P., Miller, S. L., Reponen, T., and Hernandez, M. T. (2005). Ambient Bioaerosol Indices for Indoor AirQuality Assessments of Flood Reclamation. J. Aerosol Sci. 36:763-783.
20. Farrelly, V., Rainey, F. A., and Stackebrandt, E. (1995). Effect of Genome Size and RRN Gene Copy Number on PCR Amplification of 16S Ribosomal-RNA Genes from a Mixture of Bacterial Species. Appl. Environ. Microbiol. 61:2798-2801.
21. Fierer, N., Liu, Z. Z., Rodriguez-Hernandez, M., Knight, R., Henn, M., and Hernandez, M. T. (2008). Short-Term Temporal Variability in Airborne Bacterial and Fungal Populations. Appl. Environ. Microbiol. 74:200-207.
22. Floret, N., Viel, J. F., Mauny, F., Hoen, B., and Piarroux, R. (2006). Negligible Risk for Epidemics After Geophysical Disasters. Emerging Infectious Diseases 12:543-548.
23. Frank, D. N. (2008). XplorSeq: A Software Environment for Integrated Management and Phylogenetic Analysis of Metagenomic Sequence Data. BMC Bioinformatics 9:16.
24. Frank, D. N., Spiegelman, G. B., Davis, W., Wagner, E., Lyons, E., and Pace, N. R. (2003). Culture-Independent Molecular Analysis of Microbial Constituents of the Healthy Human Outer Ear. J. Clin. Microbiol. 41:295-303.
25. Gorny, R. L., Reponen, T., Willeke, K., Schmechel, D., Robine, E., Boissier, M., and Grinshpun, S. A. (2002). Fungal Fragments as Indoor Air Biocontaminants. Appl. Environ. Microbiol. 68:3522-3531.
26. Hambraeus, A. (1988). Aerobiology in the Operating-Room-A Review. J. Hospital Infection 11:68-76.
27. Harrison, R. M., Jones, A. M., Biggins, P. D. E., Pomeroy, N., Cox, C. S., Kidd, S. P., Hobman, J. L., Brown, N. L., and Beswick, A. (2005). Climate Factors Influencing Bacterial Count in Background Air Samples. Intl. J. Biometeorology 49:167-178.
28. Hernandez, M., Miller, S. L., Landfear, D. W., and Macher, J. M. (1999). A Combined Fluorochrome Method for Quantitation of Metabolically Active and Inactive Airborne Bacteria. Aerosol Sci. Technol. 30:145-160.
29. Hongoh, Y., Yuzawa, H., Ohkuma, M., and Kudo, T. (2003). Evaluation of Primers and PCR Conditions for the Analysis of 16S rRNA Genes from a Natural Environment. FEMS Microbiol. Lett. 221:299-304.
30. Horner, W. E., Helbling, A., Salvaggio, J. E., and Lehrer, S. B. (1995). Fungal Allergens. Clin. Microbiol. Rev. 8:161-179.
31. Huber, J. A., Morrison, H. G., Huse, S.M., Neal, P. R., Sogin, M. L., andWelch, D. B. M. (2009). Effect of PCR Amplicon Size on Assessments of Clone Library Microbial Diversity and Community Structure. Environ. Microbiol. 11:1292-1302.
32. Huber, T., Faulkner, G., and Hugenholtz, P. (2004). Bellerophon: A Program to Detect Chimeric Sequences in Multiple Sequence Alignments. Bioinformatics 20:2317-2319.
33. Hughes, K. A., McCartney, H. A., Lachlan-Cope, T. A., and Pearce, D. A. (2004). A Preliminary Study of Airborne Microbial Biodiversity Over Peninsular Antarctica. Cellular and Molecular Biology 50:537-542.
34. Ishii, K., and Fukui, M. (2001). Optimization of Annealing Temperature to Reduce Bias Caused by a Primer Mismatch in Multitemplate PCR. Appl. Environ. Microbiol. 67:3753-3755.
35. Jeon, S., Bunge, J., Leslin, C., Stoeck, T., Hong, S. H., and Epstein, S. S. (2008). Environmental rRNA Inventories Miss Over Half of Protistan Diversity. BMC Microbiol. 8:13.
36. Lozupone,C., Hamady,M.,Kelley, S.T., and Knight,R. (2007).Quantitative and Qualitative Beta Diversity Measures Lead to Different Insights into Factors that Structure Microbial Communities. Appl. Environ. Microbiol. 73:1576-1585.
37. Lozupone, C., Hamady, M., and Knight, R. (2006). UniFrac-An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context. BMC Bioinformatics 7:371-385.
38. Lozupone, C., and Knight, R. (2005). UniFrac: A New Phylogenetic Method for Comparing Microbial Communities. Appl. Environ. Microbiol. 71:8228-8235.
39. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Forster, W., Brettske, I., Gerber, S., Ginhart, A. W., Gross, O., Grumann, S., Hermann, S., Jost, R., Konig, A., Liss, T., Lussmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K. H. (2004). ARB: A Software Environment for Sequence Data. Nucleic Acids Res. 32:1363-1371.
40. Madelin, T. M. (1994). Fungal Aerosols-A Review. J. Aerosol Sci. 25:1405-1412.
41. Maron, P. A., Lejon, D. P. H., Carvalho, E., Bizet, K., Lemanceau, P., Ranjard, L., and Mougel, C. (2005). Assessing Genetic Structure and Diversity of Airborne Bacterial Communities by DNA Fingerprinting and 16S rDNA Clone Library. Atmos. Environ. 39:3687-3695.
42. Maron, P. A., Mougel, C., Lejon, D. P. H., Carvalho, E., Bizet, K., Marck, G., Cubito, N., Lemanceau, P., and Ranjard, L. (2006). Temporal Variability of Airborne Bacterial Community Structure in an Urban Area. Atmos. Environ. 40:8074-8080.
43. Osborne, C. A., Galic, M., Sangwan, P., and Janssen, P. H. (2005). PCRGenerated Artefact from 16S rRNAGene-Specific Primers. FEMSMicrobiol. Lett. 248:183-187.
44. Pace, N. R. (1997). A Molecular View of Microbial Diversity and the Biosphere. Science 276:734-740.
45. Paez-Rubio, T., Viau, E., Romero-Hernandez, S., and Peccia, J. (2005). Source Bioaerosol Concentration and rRNA Gene-Based Identification of Microorganisms Aerosolized at a Flood Irrigation Wastewater Reuse Site. Appl. Environ. Microbiol. 71:804-810.
46. Papineau, D., Walker, J. J., Mojzsis, S. J., and Pace, N. R. (2005). Composition and Structure of Microbial Communities from Stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl. Environ. Microbiol. 71:4822-4832.
47. Pardue, J. H., Moe, W. M., McInnis, D., Thibodeaux, L. J., Valsaraj, K. T., Maciasz, E., van Heerden, I., Korevec, N., and Yuan, Q. Z. (2005). Chemical and Microbiological Parameters in New Orleans Floodwater Following Hurricane Katrina. Environ. Sci. Technol. 39:8591-8599.
48. Peccia, J., and Hernandez, M. (2006). Incorporating Polymerase Chain Reaction-Based Identification, Population Characterization, and Quantification of Microorganisms into Aerosol Science: A Review. Atmos. Environ. 40:3941-3961.
49. Polz, M. F., and Cavanaugh, C. M. (1998). Bias in Template-to-Product Ratios in Multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
50. Presley, S. M., Rainwater, T. R., Austin, G. P., Platt, S. G., Zak, J. C., Cobb, G. P., Marsland, E. J., Tian, K., Zhang, B. H., Anderson, T. A., Cox, S. B., Abel, M. T., Leftwich, B. D., Huddleston, J. R., Jeter, R. M., and Kendall, R. J. (2006). Assessment of Pathogens and Toxicants in New Orleans, LA Following Hurricane Katrina. Environ. Sci. Technol. 40:468-474.
51. Schloss, P. D., and Handelsman, J. (2006). Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures. Appl. Environ. Microbiol. 72:6773-6779.
52. Shultz, J. M., Russell, J., and Espinel, Z. (2005). Epidemiology of Tropical Cyclones: The Dynamics of Disaster, Disease, and Development. Epidemiologic Reviews 27:21-35.
53. Singer, E. (2005).Katrina Disease Fears Unfounded. Nature Medicine 11:1015-1015
54. Sipos, R., Szekely, A. J., Palatinszky, M., Revesz, S., Marialigeti, K., and Nikolausz, M. (2007). Effect of Primer Mismatch, Annealing Temperature and PCR Cycle Number on 16S rRNA Gene-Targetting Bacterial Community Analysis. FEMS Microbiol. Ecol. 60:341-350.
55. Suzuki,M. T., andGiovannoni, S. J. (1996).Bias Caused by Template Annealing in the Amplification ofMixtures of 16S rRNA Genes by PCR. Appl. Environ. Microbiol. 62:625-630.
56. Taylor, L. H., Latham, S. M., and Woolhouse, M. E. J. (2001). Risk Factors for Human Disease Emergence. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 356:983-989.
57. Tong, Y. Y., and Lighthart, B. (1999). Diurnal Distribution of Total and Culturable Atmospheric Bacteria at a Rural Site. Aerosol Sci. Technol. 30:246-254.
58. USACE. (2005a). Corps Marks Halfway Point in Unwatering Mission, U.S. Army Corps of Engineers, New Orleans District Public Affairs.
59. USACE. (2005b). Corps of Engineers' Update to Hurricane Katrina Response, U.S. Army Corps of Engineers, Mississippi Valley Division Public Affairs.
60. USACE. (2005c). New Orleans Water Continues to Recede over a Foot per Day, U.S. Army Corps of Engineers, New Orleans District Public Affairs.