Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

被引：123

作者：

Strong, Michael J. ^{[1
,2
]}

Xu, Guorong ^{[3
]}

Morici, Lisa ^{[4
]}

Bon-Durant, Sandra Splinter ^{[5
]}

Baddoo, Melody ^{[1
,2
]}

Lin, Zhen ^{[1
,2
]}

Fewell, Claire ^{[1
,2
]}

Taylor, Christopher M. ^{[6
,7
]}

Flemington, Erik K. ^{[1
,2
]}

机构：

[1] Tulane Univ, Dept Pathol, New Orleans, LA 70118 USA

[2] Tulane Univ, Tulane Canc Ctr, New Orleans, LA 70118 USA

[3] Univ Calif San Diego, Dept Genom Med, San Diego, CA 92103 USA

[4] Tulane Univ, Dept Microbiol & Immunol, New Orleans, LA 70118 USA

[5] Univ Wisconsin, Ctr Biotechnol, Madison, WI 53705 USA

[6] Louisiana State Univ, Sch Med, Dept Microbiol Immunol & Parasitol, New Orleans, LA USA

[7] Childrens Hosp New Orleans, Res Inst Children, New Orleans, LA USA

来源：

PLOS PATHOGENS | 2014年 / 10卷 / 11期

关键词：

EPSTEIN-BARR-VIRUS; CHINESE PATIENTS; NIH-CQV; RNA; DISCOVERY; ORIGIN;

D O I：

10.1371/journal.ppat.1004437

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.

引用

页数：6

共 32 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome [J].

Bhatt, Ami S. ;

Freeman, Samuel S. ;

Herrera, Alex F. ;

Pedamallu, Chandra Sekhar ;

Gevers, Dirk ;

Duke, Fujiko ;

Jung, Joonil ;

Michaud, Monia ;

Walker, Bruce J. ;

Young, Sarah ;

Earl, Ashlee M. ;

Kostic, Aleksander D. ;

Ojesina, Akinyemi I. ;

Hasserjian, Robert ;

Ballen, Karen K. ;

Chen, Yi-Bin ;

Hobbs, Gabriela ;

Antin, Joseph H. ;

Soiffer, Robert J. ;

Baden, Lindsey R. ;

Garrett, Wendy S. ;

Hornick, Jason L. ;

Marty, Francisco M. ;

Meyerson, Matthew .

NEW ENGLAND JOURNAL OF MEDICINE, 2013, 369 (06) :517-528

[3] Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma [J].

Castellarin, Mauro ;

Warren, Rene L. ;

Freeman, J. Douglas ;

Dreolini, Lisa ;

Krzywinski, Martin ;

Strauss, Jaclyn ;

Barnes, Rebecca ;

Watson, Peter ;

Allen-Vercoe, Emma ;

Moore, Richard A. ;

Holt, Robert A. .

GENOME RESEARCH, 2012, 22 (02) :299-306

[4]

Feng HC, 2008, SCIENCE, V319, P1096, DOI 10.1126/science.1152586

[5] Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions [J].

Fricke, W. Florian ;

Rasko, David A. .

NATURE REVIEWS GENETICS, 2014, 15 (01) :49-55

[6] Comprehensive genomic characterization of squamous cell lung cancers [J].

Hammerman, Peter S. ;

Lawrence, Michael S. ;

Voet, Douglas ;

Jing, Rui ;

Cibulskis, Kristian ;

Sivachenko, Andrey ;

Stojanov, Petar ;

McKenna, Aaron ;

Lander, Eric S. ;

Gabriel, Stacey ;

Getz, Gad ;

Sougnez, Carrie ;

Imielinski, Marcin ;

Helman, Elena ;

Hernandez, Bryan ;

Pho, Nam H. ;

Meyerson, Matthew ;

Chu, Andy ;

Chun, Hye-Jung E. ;

Mungall, Andrew J. ;

Pleasance, Erin ;

Robertson, A. Gordon ;

Sipahimalani, Payal ;

Stoll, Dominik ;

Balasundaram, Miruna ;

Birol, Inanc ;

Butterfield, Yaron S. N. ;

Chuah, Eric ;

Coope, Robin J. N. ;

Corbett, Richard ;

Dhalla, Noreen ;

Guin, Ranabir ;

Hirst, Anhe Carrie ;

Hirst, Martin ;

Holt, Robert A. ;

Lee, Darlene ;

Li, Haiyan I. ;

Mayo, Michael ;

Moore, Richard A. ;

Mungall, Karen ;

Nip, Ka Ming ;

Olshen, Adam ;

Schein, Jacqueline E. ;

Slobodan, Jared R. ;

Tam, Angela ;

Thiessen, Nina ;

Varhol, Richard ;

Zeng, Thomas ;

Zhao, Yongjun ;

Jones, Steven J. M. .

NATURE, 2012, 489 (7417) :519-525

[7] Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples [J].

Hasman, Henrik ;

Saputra, Dhany ;

Sicheritz-Ponten, Thomas ;

Lund, Ole ;

Svendsen, Christina Aaby ;

Frimodt-Moller, Niels ;

Aarestrup, Frank M. .

JOURNAL OF CLINICAL MICROBIOLOGY, 2014, 52 (01) :139-146

[8] Comprehensive molecular portraits of human breast tumours [J].

Koboldt, Daniel C. ;

Fulton, Robert S. ;

McLellan, Michael D. ;

Schmidt, Heather ;

Kalicki-Veizer, Joelle ;

McMichael, Joshua F. ;

Fulton, Lucinda L. ;

Dooling, David J. ;

Ding, Li ;

Mardis, Elaine R. ;

Wilson, Richard K. ;

Ally, Adrian ;

Balasundaram, Miruna ;

Butterfield, Yaron S. N. ;

Carlsen, Rebecca ;

Carter, Candace ;

Chu, Andy ;

Chuah, Eric ;

Chun, Hye-Jung E. ;

Coope, Robin J. N. ;

Dhalla, Noreen ;

Guin, Ranabir ;

Hirst, Carrie ;

Hirst, Martin ;

Holt, Robert A. ;

Lee, Darlene ;

Li, Haiyan I. ;

Mayo, Michael ;

Moore, Richard A. ;

Mungall, Andrew J. ;

Pleasance, Erin ;

Robertson, A. Gordon ;

Schein, Jacqueline E. ;

Shafiei, Arash ;

Sipahimalani, Payal ;

Slobodan, Jared R. ;

Stoll, Dominik ;

Tam, Angela ;

Thiessen, Nina ;

Varhol, Richard J. ;

Wye, Natasja ;

Zeng, Thomas ;

Zhao, Yongjun ;

Birol, Inanc ;

Jones, Steven J. M. ;

Marra, Marco A. ;

Cherniack, Andrew D. ;

Saksena, Gordon ;

Onofrio, Robert C. ;

Pho, Nam H. .

NATURE, 2012, 490 (7418) :61-70

[9] Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology [J].

Koeser, Claudio U. ;

Ellington, Matthew J. ;

Cartwright, Edward J. P. ;

Gillespie, Stephen H. ;

Brown, Nicholas M. ;

Farrington, Mark ;

Holden, Matthew T. G. ;

Dougan, Gordon ;

Bentley, Stephen D. ;

Parkhill, Julian ;

Peacock, Sharon J. .

PLOS PATHOGENS, 2012, 8 (08)

[10] Genomic analysis identifies association of Fusobacterium with colorectal carcinoma [J].

Kostic, Aleksandar D. ;

Gevers, Dirk ;

Pedamallu, Chandra Sekhar ;

Michaud, Monia ;

Duke, Fujiko ;

Earl, Ashlee M. ;

Ojesina, Akinyemi I. ;

Jung, Joonil ;

Bass, Adam J. ;

Tabernero, Josep ;

Baselga, Jose ;

Liu, Chen ;

Shivdasani, Ramesh A. ;

Ogino, Shuji ;

Birren, Bruce W. ;

Huttenhower, Curtis ;

Garrett, Wendy S. ;

Meyerson, Matthew .

GENOME RESEARCH, 2012, 22 (02) :292-298

← 1 2 3 4 →