title: Clinical microbiology informatics.
abstract: The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA danrhoads@gmail.com.
authors.forename: Daniel D
authors.initials: DD
authors.lastname: Rhoads
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia.
authors.forename: Vitali
authors.initials: V
authors.lastname: Sintchenko
authors.affiliation: Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Rauch
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.
authors.forename: Liron
authors.initials: L
authors.lastname: Pantanowitz
mesh_terms: D057205:Automation, Laboratory; D002984:Clinical Laboratory Information Systems / Q000295:instrumentation; D018563:Disease Notification; D006801:Humans; D008490:Medical Informatics / Q000295:instrumentation / Q000379:methods; D008828:Microbiological Techniques / Q000295:instrumentation / Q000379:methods; D008829:Microbiology / Q000295:instrumentation / Q000592:standards