title: Widespread colonization of the lung by Tropheryma whipplei in HIV infection.
abstract: BACKGROUND
  Lung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV.
  
  
  OBJECTIVE
  To determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota.
  
  
  METHODS
  We used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects.
  
  
  RESULTS
  Sequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease.
  
  
  CONCLUSIONS
  Asymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.
authors: Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA.
authors: Catherine
authors: C
authors: Lozupone
authors: Adela
authors: A
authors: Cota-Gomez
authors: Brent E
authors: BE
authors: Palmer
authors: Derek J
authors: DJ
authors: Linderman
authors: Emily S
authors: ES
authors: Charlson
authors: Erica
authors: E
authors: Sodergren
authors: Makedonka
authors: M
authors: Mitreva
authors: Sahar
authors: S
authors: Abubucker
authors: John
authors: J
authors: Martin
authors: Guohui
authors: G
authors: Yao
authors: Thomas B
authors: TB
authors: Campbell
authors: Sonia C
authors: SC
authors: Flores
authors: Gail
authors: G
authors: Ackerman
authors: Jesse
authors: J
authors: Stombaugh
authors: Luke
authors: L
authors: Ursell
authors: James M
authors: JM
authors: Beck
authors: Jeffrey L
authors: JL
authors: Curtis
authors: Vincent B
authors: VB
authors: Young
authors: Susan V
authors: SV
authors: Lynch
authors: Laurence
authors: L
authors: Huang
authors: George M
authors: GM
authors: Weinstock
authors: Kenneth S
authors: KS
authors: Knox
authors: Homer
authors: H
authors: Twigg
authors: Alison
authors: A
authors: Morris
authors: Elodie
authors: E
authors: Ghedin
authors: Frederic D
authors: FD
authors: Bushman
authors: Ronald G
authors: RG
authors: Collman
authors: Rob
authors: R
authors: Knight
authors: Andrew P
authors: AP
authors: Fontenot
mesh_terms: D015331:Cohort Studies; D015658:HIV Infections / Q000150:complications*; D006801:Humans; D008137:Longitudinal Studies; D008168:Lung / Q000382:microbiology*; D054851:Tropheryma; D008061:Whipple Disease / Q000150:complications* / Q000382:microbiology*
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