title: Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections.
abstract: BACKGROUND
  Cystic fibrosis (CF) airways are colonized by a polymicrobial community of organisms, termed the CF microbiota. We sought to define the microbial constituents of the home environment of individuals with CF and determine if it may serve as a latent reservoir for infection.
  
  
  METHODS
  Six patients with newly identified CF pathogens were included. An investigator collected repeat sputum and multiple environmental samples from their homes. Bacteria were cultured under both aerobic and anaerobic conditions. Morphologically distinct colonies were selected, purified and identified to the genus and species level through 16S rRNA gene sequencing. When concordant organisms were identified in sputum and environment, pulsed-field gel electrophoresis (PFGE) was performed to determine relatedness. Culture-independent bacterial profiling of each sample was carried out by Illumina sequencing of the V3 region of the 16s RNA gene.
  
  
  RESULTS
  New respiratory pathogens prompting investigation included: Mycobacterium abscessus(2), Stenotrophomonas maltophilia(3), Pseudomonas aeruginosa(3), Pseudomonas fluorescens(1), Nocardia spp.(1), and Achromobacter xylosoxidans(1). A median 25 organisms/patient were cultured from sputum. A median 125 organisms/home were cultured from environmental sites. Several organisms commonly found in the CF lung microbiome were identified within the home environments of these patients. Concordant species included members of the following genera: Brevibacterium(1), Microbacterium(1), Staphylococcus(3), Stenotrophomonas(2), Streptococcus(2), Sphingomonas(1), and Pseudomonas(4). PFGE confirmed related strains (one episode each of Sphinogomonas and P. aeruginosa) from the environment and airways were identified in two patients. Culture-independent assessment confirmed that many organisms were not identified using culture-dependent techniques.
  
  
  CONCLUSIONS
  Members of the CF microbiota can be found as constituents of the home environment in individuals with CF. While the majority of isolates from the home environment were not genetically related to those isolated from the lower airways of individuals with CF suggesting alternate sources of infection were more common, a few genetically related isolates were indeed identified. As such, the home environment may rarely serve as either the source of infection or a persistent reservoir for re-infection after clearance.
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.|Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
authors: Alya
authors: A
authors: Heirali
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
authors: Suzanne
authors: S
authors: McKeon
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
authors: Swathi
authors: S
authors: Purighalla
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.|Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
authors: Douglas G
authors: DG
authors: Storey
authors: The Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
authors: Laura
authors: L
authors: Rossi
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
authors: Geoffrey
authors: G
authors: Costilhes
authors: Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, Canada.
authors: Steven J
authors: SJ
authors: Drews
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.|Department of Medicine, The University of Calgary, Calgary, AB, Canada.
authors: Harvey R
authors: HR
authors: Rabin
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.|The Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
authors: Michael G
authors: MG
authors: Surette
authors: Department of Microbiology Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.|Department of Medicine, The University of Calgary, Calgary, AB, Canada.
authors: Michael D
authors: MD
authors: Parkins
mesh_terms: D000328:Adult; D000368:Aged; D015373:Bacterial Typing Techniques; D003550:Cystic Fibrosis / Q000150:complications* / Q000382:microbiology*; D004197:Disease Reservoirs / Q000382:microbiology; D004783:Environmental Microbiology; D005260:Female; D005798:Genes, Bacterial; D006798:Housing; D006801:Humans; D008297:Male; D064307:Microbiota / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification; D012141:Respiratory Tract Infections / Q000209:etiology* / Q000382:microbiology*; D013183:Sputum / Q000382:microbiology; D055815:Young Adult
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S