Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens.
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria.
Mina
M
Bashir
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA.
Mahjabeen
M
Ahmed
Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria.
Thomas
T
Weinmaier
Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
Doina
D
Ciobanu
Department of Energy, Joint Genome Institute Walnut Creek, CA, USA.
Natalia
N
Ivanova
Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria.
Thomas R
TR
Pieber
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA.
Parag A
PA
Vaishampayan
Acinetobacter; cleanroom; functional metagenomics; indoor environments; microbiome; pathogens; spacecraft; virulence factors
Cell Syst. 2015 Jul 29;1(1):72-87
26594662
Astrobiology. 2014 Oct;14(10):837-47
25243569
Appl Environ Microbiol. 2007 Apr;73(8):2600-11
17308177
PDA J Pharm Sci Technol. 2011 Jul-Aug;65(4):392-403
22293526
Appl Environ Microbiol. 1980 Jan;39(1):159-64
7188846
PLoS One. 2013 Jun 12;8(6):e65388
23776475
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
10592173
PLoS One. 2015 Aug 14;10(8):e0134848
26273838
Bioinformatics. 2014 Mar 1;30(5):614-20
24142950
Microbiome. 2015 Dec 08;3:62
26642878
ISME J. 2013 Feb;7(2):312-24
23051695
PLoS One. 2013;8(3):e57730
23483923
Antimicrob Agents Chemother. 2013 Jul;57(7):2989-95
23587960
Zoonoses Public Health. 2012 Sep;59 Suppl 2:158-65
22958260
Microbiome. 2015 Oct 13;3:49
26459172
Appl Environ Microbiol. 1980 Sep;40(3):480-5
7191692
Appl Environ Microbiol. 2009 Oct;75(20):6559-67
19700540
Astrobiology. 2012 May;12(5):487-97
22680694
Microbes Infect. 2003 Jun;5(7):651-7
12787741
PLoS One. 2015 Oct 28;10(10):e0141399
26509793
Science. 2014 Aug 29;345(6200):1048-52
25170151
Appl Environ Microbiol. 2007 Jan;73(1):278-88
17071787
Front Microbiol. 2013 Aug 05;4:221
23935596
Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):165-72
12656168
Front Microbiol. 2011 Apr 25;2:74
21747794
Nat Methods. 2010 May;7(5):335-6
20383131
Astrobiology. 2010 Jun;10(5):499-508
20624058
Genome Res. 2007 Mar;17(3):377-86
17255551
Sensors (Basel). 2015 Sep 16;15(9):23418-30
26389913
Microbiome. 2015 Oct 27;3:50
26502721
BMC Bioinformatics. 2011 Sep 30;12:385
21961884
Bioinformatics. 2011 Mar 15;27(6):863-4
21278185
Emerg Infect Dis. 2012 May;18(5):741-9
22515968
Folia Histochem Cytobiol. 2008;46(3):257-67
19056528
Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6
11959976
Nucleic Acids Res. 2007 Jan;35(Database issue):D391-4
17090593
Astrobiology. 2010 Apr;10(3):325-35
20446872
Clin Microbiol Rev. 2004 Jan;17(1):14-56
14726454
Sci Rep. 2015 Mar 17;5:9156
25778463
Int J Syst Evol Microbiol. 2010 May;60(Pt 5):1031-7
19666815
Indian J Med Res. 2011 Feb;133:195-200
21415494
Eur J Nutr. 2016 Jun;55(4):1479-89
26130323
Infect Immun. 1999 Jul;67(7):3662-6
10377156
PLoS One. 2011;6(10):e26161
22028825
Clin Infect Dis. 2009 Jan 1;48(1):1-12
19035777
Nat Methods. 2015 Jan;12(1):59-60
25402007
Int J Biometeorol. 1998 Aug;42(1):1-7
9780844
Microb Ecol. 2004 Feb;47(2):150-8
14749906
J Infect Dis. 2008 Apr 15;197(8):1079-81
18419525
J Bacteriol. 2009 Sep;191(18):5584-91
19592590
FEMS Microbiol Ecol. 2007 Sep;61(3):509-21
17655710
PLoS One. 2008 Apr 02;3(4):e1862
18382653
Environ Microbiol. 2014 Mar;16(3):643-57
24372985
Nucleic Acids Res. 2014 Jan;42(Database issue):D199-205
24214961
ISME J. 2011 Feb;5(2):209-19
20703318