title: Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.
abstract: 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.
authors.affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Strong
authors.affiliation: Department of Genomic Medicine, University of California, San Diego, California, United States of America.
authors.forename: Guorong
authors.initials: G
authors.lastname: Xu
authors.affiliation: Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Lisa
authors.initials: L
authors.lastname: Morici
authors.affiliation: University of Wisconsin Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Sandra
authors.initials: S
authors.lastname: Splinter Bon-Durant
authors.affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Melody
authors.initials: M
authors.lastname: Baddoo
authors.affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Claire
authors.initials: C
authors.lastname: Fewell
authors.affiliation: Department of Microbiology, Immunology & Parasitology, Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America; Research Institute for Children, Children's Hospital of New Orleans, New Orleans, Louisiana, United States of America.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Taylor
authors.affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America; Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America.
authors.forename: Erik K
authors.initials: EK
authors.lastname: Flemington
mesh_terms: D030561:Databases, Nucleic Acid; D004866:Equipment Contamination; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007239:Infections / Q000175:diagnosis* / Q000235:genetics*