title: Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness.
abstract: We examined the microbial composition in the diseased lung and early-phase microbial cultures from the blood of a patient with a rapidly progressing fatal pulmonary illness. Although no microbes could be isolated from such cultures during the initial study, the HTS-microbiome study revealed the presence of a unique mixture of alphaproteobacteria, composed mainly of different families of Rhizobiales microbes. Microbial 16S rDNA sequences matching closely to Afipia cberi were identified mainly in the patient's diseased lung tissue, but only rarely in the early-phase blood cultures. Conversely, the high abundance of sequences found in early-phase blood cultures of different broth media matched closely with those of the families Methylobacteriaceae, Phyllobacteriaceae and Sphingomonadaceae. The two species that successfully adapted to grow in a laboratory culture system were A. cberi and Mesorhizobium hominis, which eventually were isolated from a previously cryopreserved blood culture of SP4 broth. Many other species, including members of the Bradyrhizobiaceae and Phyllobacteriaceae families, and all members of the Methylobacteriaceae and Sphingomonadaceae families identified by HTS remained non-cultivated. We developed specific PCR primers and FISH probes, which detected the target Rhizobiales microbes in former blood cultures and autopsy lung tissues. It is unclear what role these Rhizobiales microbes might have played in the patient's complex disease process. However, the above mentioned assays should help in rapidly detecting and identifying these previously unrecognized Rhizobiales microbes in patients.
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Shyh-Ching
authors.initials: SC
authors.lastname: Lo
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Guo-Chiuan
authors.initials: GC
authors.lastname: Hung
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Bingjie
authors.initials: B
authors.lastname: Li
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Lei
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Tianwei
authors.initials: T
authors.lastname: Li
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Nagamine
authors.affiliation: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration Silver Spring, Maryland 20993, USA.
authors.forename: Shien
authors.initials: S
authors.lastname: Tsai
authors.affiliation: Department of Medicine, Newark Beth Israel Medical Center Newark, New Jersey 07112, USA.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Zucker
authors.affiliation: Department of Pathology, Newark Beth Israel Medical Center Newark, New Jersey 07112, USA.
authors.forename: Ludmilla
authors.initials: L
authors.lastname: Olesnicky
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001344:Autopsy; D016470:Bacteremia / Q000382:microbiology*; D001483:Base Sequence; D045744:Cell Line, Tumor; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D017809:Fatal Outcome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008168:Lung / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012141:Respiratory Tract Infections / Q000097:blood / Q000175:diagnosis / Q000382:microbiology*; D021521:Ribotyping
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Afipia; Bradyrhizobiaceae; HTS; MPS; Mesorhizobium; Methylobacteriaceae; Microbiome; Phyllobacteriaceae; Rhizobiales; Sphingomonadaceae; alphaproteobacteria
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