Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung

Abstract

Microbial communities in the lungs of patients with cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) have been shown to be spatially heterogeneous. Viral communities may also vary spatially, leading to localized viral populations and infections. Here, we characterized viral communities from multiple areas of the lungs of two patients with late-stage CF using metagenomics, that is, the explanted lungs from a transplant patient and lungs acquired postmortem. All regions harbored eukaryotic viruses that may infect the human host, notably herpesviruses, anelloviruses, and papillomaviruses. In the highly diseased apical lobes of explant lungs, viral diversity was extremely low, and only eukaryotic viruses were present. The absence of phage suggests that CF-associated microbial biofilms may escape top-down controls by phage predation. The phages present in other lobes of explant lungs and in all lobes of postmortem lungs comprised distinct communities, and encoded genes for clinically important microbial phenotypes, including small colony variants and antibiotic resistance. Based on the these observations, we postulate that viral communities in CF lungs are spatially distinct and contribute to CF pathology by augmenting the metabolic potential of resident microbes, as well as by directly damaging lung tissue via carcinomas and herpesviral outbreaks.

Figure 1.

Flow chart for lung dissection and subsequent sample processing. PCR, polymerase chain reaction; SDSU, San Diego State University; UCSD, University of California at San Diego.

Figure 2.

General characteristics of lung viromes. (A) Number of base pairs of sequenced viral DNA per lobe, and percentage of known/unknown sequences in each lobe. (B) Predicted host domains for known sequences in each lobe are shown as the percentage of annotated viral sequences attributed to a particular domain. (C) Predicted hosts of phages identified in each lobe. Ling, lingula; LLL, left lower lobe; LLLA, left lower lobe, anterior; LLLP, left lower lobe, posterior; LUL, left upper lobe; RLL, right lower lobe; RML, right middle lobe; RUL, right upper lobe.

Figure 3.

Eukaryotic viruses in the cystic fibrosis lung. (A) Human papillomavirus (HPV) genome. The left lower lobe of the explant lung provided an approximately ×15 coverage of HPV49. (B) Torque teno virus (TTV), with an approximately ×14 coverage in the virome from the right middle lobe (RML) of the postmortem lung. (C) Anellovirus. ORF, open reading frame.

Figure 4.

Spatial distribution of antibiotic resistance genes in the viromes from the explant (A) and postmortem (B) lungs.