title: Current and future molecular diagnostics for ocular infectious diseases.
abstract: OBJECTIVE
  Confirmation of ocular infections can pose great challenges to the clinician. A fundamental limitation is the small amounts of specimen that can be obtained from the eye. Molecular diagnostics can circumvent this limitation and have been shown to be more sensitive than conventional culture. The purpose of this review is to describe new molecular methods and to discuss the applications of next-generation sequencing-based approaches in the diagnosis of ocular infections.
  
  
  RESULTS
  Efforts have focused on improving the sensitivity of pathogen detection using molecular methods. This review describes a new molecular target for Toxoplasma gondii-directed polymerase chain reaction assays. Molecular diagnostics for Chlamydia trachomatis and Acanthamoeba species are also discussed. Finally, we describe a hypothesis-free approach, metagenomic deep sequencing, which can detect DNA and RNA pathogens from a single specimen in one test. In some cases, this method can provide the geographic location and timing of the infection.
  
  
  CONCLUSIONS
  Pathogen-directed PCRs have been powerful tools in the diagnosis of ocular infections for over 20 years. The use of next-generation sequencing-based approaches, when available, will further improve sensitivity of detection with the potential to improve patient care.
authors: aF.I. Proctor Foundation bDepartment of Ophthalmology, University of California, San Francisco cDepartment of Pathology dDivision of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.
authors: Thuy
authors: T
authors: Doan
authors: Benjamin A
authors: BA
authors: Pinsky
mesh_terms: D000048:Acanthamoeba / Q000235:genetics; D000562:Amebiasis / Q000150:complications / Q000175:diagnosis; D002690:Chlamydia Infections / Q000150:complications / Q000175:diagnosis*; D002692:Chlamydia trachomatis / Q000235:genetics*; D015817:Eye Infections / Q000175:diagnosis* / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054892:Metagenome; D025202:Molecular Diagnostic Techniques / Q000379:methods* / Q000639:trends; D016133:Polymerase Chain Reaction; D014122:Toxoplasma / Q000235:genetics; D014123:Toxoplasmosis / Q000150:complications / Q000175:diagnosis*