PROJECT INFORMATION
GOLD Project ID
Gp0145372  
Project Name
Acinetobacter baumannii Pulsotype 27  
Other Names
  
Legacy GOLD ID
  
NCBI BioProject Name Genomic Epidemiology of a hospital outbreak of MDR Acinetobacter baumannii
NCBI BioProject ID 259902
NCBI BioProject Accession PRJEB4735
NCBI Locus Tag
AB2012  
NCBI BioSample Accession SAMEA3139099
PI
Added By JGI automated process on 2016-05-18
Last Modified By Supratim Mukherjee on 2017-03-29
Project Comments
  
Project Status
Permanent Draft  
Project Relevance
  
Sequencing Center UW
Collaborating Institute
  
Funding Agency
  
Project Description
BACKGROUND Multi-drug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within any given outbreak, it can be difficult to identify the precise mechanisms and sources of infection rapidly and accurately enough to inform infection control teams how best to terminate an outbreak. Here we describe a protracted hospital outbreak of multidrug-resistant A. baumannii, in which whole-genome sequencing (WGS) was used to obtain a high-resolution view of the relationships between isolates, allowing us to reconstruct chains of transmission, confirm or refute epidemiological hypotheses and to provide the infection control team with useful insights into the sources and routes of infection during this outbreak. METHODS 117 putative Acinetobacter isolates obtained from 59 patients and 10 environmental swabs were genome-sequenced on the Illumina MiSeq. Genomes were mapped against a reference sequence for the outbreak strain to identify single-nucleotide polymorphisms (SNPs). A combination of SNP genotype and conventional epidemiologic analysis was used to reconstruct a parsimonious set of transmission events. RESULTS The outbreak strain was found to be distinct from other genome-sequenced strains. We identified 31 SNPs among isolates from the outbreak and defined six major SNP-based genotypic clusters within the outbreak, together with one additional genotype defined by loss of a plasmid. We were able to rule seventeen isolates out of the outbreak. We documented within-host diversity in several patients, including mixtures of unrelated Acinetobacter strains and within-strain clouds of SNP diversity. Using genome sequence data and conventional epidemiology, we were able to reconstruct 67 transmission events that linked all but seven of the patients. We were also able to link patient-derived isolates directly to environmental isolates. These efforts focused our attention on a contaminated bed and a burns operating theatre as sources of transmission, which led to improvements in decontamination protocols. CONCLUSIONS With falling costs and higher throughput, WGS is now poised to make a decisive impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant timeframe and allowing infection control teams to track, and even prevent, the spread of multi-drug-resistant hospital pathogens.  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
PROJECT COMPOSITION
Study Genomic Epidemiology of a Protracted Hospital Outbreak caused by Multi-Drug-Resistant Acinetobacter baumannii
Organism Acinetobacter baumannii Pulsotype 27
Analysis Projects Acinetobacter baumannii Pulsotype 27
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31)
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0140266
Organism Name
Acinetobacter baumannii Pulsotype 27  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
PROTEOBACTERIA-GAMMA  
Genus
Acinetobacter  
Genus Synonyms
  
Species
Acinetobacter baumannii  
Subspecies
  
Species Synonyms
  
Strain
Pulsotype 27  
Strain Synonyms
  
Serovar-Biovar
  
Culture Collection ID
  
Type Strain
  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 1449755
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Proteobacteria  
NCBI Class
Gammaproteobacteria  
NCBI Order
Pseudomonadales  
NCBI Family
Moraxellaceae  
NCBI Genus
Acinetobacter  
NCBI Species
Acinetobacter baumannii  
ISOLATION CLASSIFICATION
Ecosystem
  
Ecosystem Category
  
Ecosystem Type
  
Ecosystem Subtype
  
Specific Ecosystem
  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
  
Temperature Optimum
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

  You are going to add the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  You are going to remove permissions for the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  Changing the SP visibility will also change visibility on the following items:

 

Do you want to continue with this visibility change?

 

 

  Checking that this Sequencing Project can be made private:

 

Do you want to continue with this visibility change?