Changes in the lung microbiome following lung transplantation include the emergence of two distinct Pseudomonas species with distinct clinical associations.
BACKGROUND
Multiple independent culture-based studies have identified the presence of Pseudomonas aeruginosa in respiratory samples as a positive risk factor for bronchiolitis obliterans syndrome (BOS). Yet, culture-independent microbiological techniques have identified a negative association between Pseudomonas species and BOS. Our objective was to investigate whether there may be a unifying explanation for these apparently dichotomous results.


METHODS
We performed bronchoscopies with bronchoalveolar lavage (BAL) on lung transplant recipients (46 procedures in 33 patients) and 26 non-transplant control subjects. We analyzed bacterial communities in the BAL fluid using qPCR and pyrosequencing of 16S rRNA gene amplicons and compared the culture-independent data with the clinical metadata and culture results from these subjects.


RESULTS
Route of bronchoscopy (via nose or via mouth) was not associated with changes in BAL microbiota (p = 0.90). Among the subjects with positive Pseudomonas bacterial culture, P. aeruginosa was also identified by culture-independent methods. In contrast, a distinct Pseudomonas species, P. fluorescens, was often identified in asymptomatic transplant subjects by pyrosequencing but not detected via standard bacterial culture. The subject populations harboring these two distinct pseudomonads differed significantly with respect to associated symptoms, BAL neutrophilia, bacterial DNA burden and microbial diversity. Despite notable differences in culturability, a global database search of UM Hospital Clinical Microbiology Laboratory records indicated that P. fluorescens is commonly isolated from respiratory specimens.


CONCLUSIONS
We have reported for the first time that two prominent and distinct Pseudomonas species (P. fluorescens and P. aeruginosa) exist within the post-transplant lung microbiome, each with unique genomic and microbiologic features and widely divergent clinical associations, including presence during acute infection.
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Robert P
RP
Dickson
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
John R
JR
Erb-Downward
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Research Service, Department of Veterans Affairs Health Care System, Ann Arbor, Michigan, United States of America.
Christine M
CM
Freeman
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Natalie
N
Walker
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Brittan S
BS
Scales
Department of Medicine, University of Colorado Denver, Aurora, Colorado and Medicine Service, Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, United States of America.
James M
JM
Beck
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Fernando J
FJ
Martinez
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Pulmonary & Critical Care Medicine Section, Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America.
Jeffrey L
JL
Curtis
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Vibha N
VN
Lama
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
Gary B
GB
Huffnagle
D000328:Adult; D000368:Aged; D001989:Bronchiolitis Obliterans / Q000209:etiology / Q000382:microbiology*; D018893:Bronchoalveolar Lavage; D016022:Case-Control Studies; D005260:Female; D006801:Humans; D008168:Lung / Q000382:microbiology*; D008171:Lung Diseases / Q000382:microbiology / Q000628:therapy*; D016040:Lung Transplantation; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011183:Postoperative Complications; D011549:Pseudomonas / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D055815:Young Adult
D012336:RNA, Ribosomal, 16S