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.
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.
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.
Alexander L
AL
Greninger
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Jessica
J
Streithorst
Department of Medicine, Division of Pulmonology, University of California San Francisco, San Francisco, CA, USA.
Jeffrey A
JA
Golden
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.
Charles Y
CY
Chiu
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.
Steve
S
Miller
D001482:Base Composition; D019121:Burkholderia Infections / Q000382:microbiology*; D042521:Burkholderiaceae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D003550:Cystic Fibrosis / Q000150:complications*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008297:Male; D009154:Mutation; D017422:Sequence Analysis, DNA; D013997:Time Factors; D055815:Young Adult
D004269:DNA, Bacterial
Genome sequence; Pandoraea apista; Strain evolution