Complete genome sequence of sequential Pandoraea apista isolates from the same cystic fibrosis patient supports a model of chronic colonization with in vivo strain evolution over time

Alexander L Greninger; Jessica Streithorst; Jeffrey A Golden; Charles Y Chiu; Steve Miller

doi:10.1016/j.diagmicrobio.2016.10.013

Complete genome sequence of sequential Pandoraea apista isolates from the same cystic fibrosis patient supports a model of chronic colonization with in vivo strain evolution over time

Diagn Microbiol Infect Dis. 2017 Jan;87(1):1-6. doi: 10.1016/j.diagmicrobio.2016.10.013. Epub 2016 Oct 11.

Authors

Alexander L Greninger¹, Jessica Streithorst², Jeffrey A Golden³, Charles Y Chiu⁴, Steve Miller⁵

Affiliations

¹ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
² Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
³ Department of Medicine, Division of Pulmonology, University of California San Francisco, San Francisco, CA, USA.
⁴ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
⁵ Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. Electronic address: steve.miller@ucsf.edu.

PMID: 28336132
DOI: 10.1016/j.diagmicrobio.2016.10.013

Abstract

Pandoraea apista in the family Burkholderiaceae is an emerging opportunistic pathogen in cystic fibrosis patients. Here, we describe a case from which 3 separate isolates of P. apista were recovered over a 1-year period. Using a combination of first-, second-, and third-generation sequencing technologies, we sequenced and de novo assembled the complete genomes of these 3 P. apista isolates. The genome of P. apista TF81F4 sequenced in this study was 5.58 Mb with a GC% of 62.3%, differed in sequence from other Pandoraea species by >20%, and included a number of previously undescribed loci. Three P. apista isolates cultured over a 12-month period were >99.999% identical by nucleotide, consistent with a model of chronic colonization by a single strain. Over time, the isolates accumulated point mutations, deletions, and insertions in a stepwise fashion, indicating in vivo strain evolution within the cystic fibrosis lung niche.

Keywords: Genome sequence; Pandoraea apista; Strain evolution.

Publication types

Case Reports

MeSH terms

Base Composition
Burkholderia Infections / microbiology*
Burkholderiaceae / classification
Burkholderiaceae / genetics
Burkholderiaceae / isolation & purification*
Cystic Fibrosis / complications*
DNA, Bacterial / chemistry
DNA, Bacterial / genetics*
Evolution, Molecular*
Genetic Variation*
Genome, Bacterial*
Genotype
Humans
Male
Mutation
Sequence Analysis, DNA
Time Factors
Young Adult

Substances

DNA, Bacterial