title: Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments.
abstract: BACKGROUND
  High-throughput genomic technologies offer new approaches for environmental health monitoring, including metagenomic surveillance of antibiotic resistance determinants (ARDs). Although natural environments serve as reservoirs for antibiotic resistance genes that can be transferred to pathogenic and human commensal bacteria, monitoring of these determinants has been infrequent and incomplete. Furthermore, surveillance efforts have not been integrated into public health decision making.
  
  
  OBJECTIVE
  We used a metagenomic epidemiology-based approach to develop an ARD index that quantifies antibiotic resistance potential, and we analyzed this index for common modal patterns across environmental samples. We also explored how metagenomic data such as this index could be conceptually framed within an early risk management context.
  
  
  METHODS
  We analyzed 25 published data sets from shotgun pyrosequencing projects. The samples consisted of microbial community DNA collected from marine and freshwater environments across a gradient of human impact. We used principal component analysis to identify index patterns across samples.
  
  
  RESULTS
  We observed significant differences in the overall index and index subcategory levels when comparing ecosystems more proximal versus distal to human impact. The selection of different sequence similarity thresholds strongly influenced the index measurements. Unique index subcategory modes distinguished the different metagenomes.
  
  
  CONCLUSIONS
  Broad-scale screening of ARD potential using this index revealed utility for framing environmental health monitoring and surveillance. This approach holds promise as a screening tool for establishing baseline ARD levels that can be used to inform and prioritize decision making regarding management of ARD sources and human exposure routes.
  
  
  BACKGROUND
  Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM. 2014. Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect 122:222–228; http://dx.doi.org/10.1289/ehp.1307009
authors: Department of Environmental and Occupational Health Sciences, and.
authors: Jesse A
authors: JA
authors: Port
authors: Alison C
authors: AC
authors: Cullen
authors: James C
authors: JC
authors: Wallace
authors: Marissa N
authors: MN
authors: Smith
authors: Elaine M
authors: EM
authors: Faustman
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics; D004352:Drug Resistance, Microbial; D017753:Ecosystem; D004784:Environmental Monitoring / Q000379:methods*; D005618:Fresh Water / Q000382:microbiology; D007194:India; D054892:Metagenome; D025341:Principal Component Analysis; D062486:Public Health Surveillance / Q000379:methods*; D012623:Seawater / Q000382:microbiology; D014481:United States
chemical_list: D000900:Anti-Bacterial Agents