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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.

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.
PMID
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Authors

Mayor MeshTerms

Evolution, Molecular

Genetic Variation

Genome, Bacterial

Keywords

Genome sequence

Pandoraea apista

Strain evolution

Journal Title diagnostic microbiology and infectious disease
Publication Year Start




PMID- 28336132
OWN - NLM
STAT- MEDLINE
DA  - 20170324
DCOM- 20170417
LR  - 20170417
IS  - 1879-0070 (Electronic)
IS  - 0732-8893 (Linking)
VI  - 87
IP  - 1
DP  - 2017 Jan
TI  - 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.
PG  - 1-6
LID - S0732-8893(16)30337-6 [pii]
LID - 10.1016/j.diagmicrobio.2016.10.013 [doi]
AB  - 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.
CI  - Copyright (c) 2016 Elsevier Inc. All rights reserved.
FAU - Greninger, Alexander L
AU  - Greninger AL
AD  - 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.
FAU - Streithorst, Jessica
AU  - Streithorst J
AD  - Department of Laboratory Medicine, University of California San Francisco, San
      Francisco, CA, USA.
FAU - Golden, Jeffrey A
AU  - Golden JA
AD  - Department of Medicine, Division of Pulmonology, University of California San
      Francisco, San Francisco, CA, USA.
FAU - Chiu, Charles Y
AU  - Chiu CY
AD  - 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.
FAU - Miller, Steve
AU  - Miller S
AD  - 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: [email protected]
LA  - eng
PT  - Case Reports
PT  - Journal Article
DEP - 20161011
PL  - United States
TA  - Diagn Microbiol Infect Dis
JT  - Diagnostic microbiology and infectious disease
JID - 8305899
RN  - 0 (DNA, Bacterial)
SB  - IM
MH  - Base Composition
MH  - Burkholderia Infections/*microbiology
MH  - Burkholderiaceae/classification/genetics/*isolation & purification
MH  - Cystic Fibrosis/*complications
MH  - DNA, Bacterial/chemistry/*genetics
MH  - *Evolution, Molecular
MH  - *Genetic Variation
MH  - *Genome, Bacterial
MH  - Genotype
MH  - Humans
MH  - Male
MH  - Mutation
MH  - Sequence Analysis, DNA
MH  - Time Factors
MH  - Young Adult
OTO - NOTNLM
OT  - *Genome sequence
OT  - *Pandoraea apista
OT  - *Strain evolution
EDAT- 2017/03/25 06:00
MHDA- 2017/04/18 06:00
CRDT- 2017/03/25 06:00
PHST- 2016/08/31 [received]
PHST- 2016/10/07 [revised]
PHST- 2016/10/07 [accepted]
AID - S0732-8893(16)30337-6 [pii]
AID - 10.1016/j.diagmicrobio.2016.10.013 [doi]
PST - ppublish
SO  - Diagn Microbiol Infect Dis. 2017 Jan;87(1):1-6. doi:
      10.1016/j.diagmicrobio.2016.10.013. Epub 2016 Oct 11.

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