Clinical Microbiology Informatics

Abstract

SUMMARY 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.

Clinical and laboratory considerations for the rapid detection of carbapenem-resistant Enterobacteriaceae

“…Rapid testing for CRE highlights the importance of clinical microbiology informatics, or the ability to integrate result reporting, communication to clinicians, and clinical decision support systems (CDSSs) in order to optimize patient outcomes. 85 CDSSs can take many forms, including comprehensive computerized disease management systems that can integrate clinical data, medication orders, and laboratory and microbiology results to suggest anti-infective therapy and alert clinicians about potential suboptimal management of infections. [86][87][88][89] Several studies of rapid blood culture diagnostics report favorable outcomes when rapid test results are reported together with CDSSs that provide actionable guidance for clinicians through antimicrobial stewardship team oversight [90][91][92][93][94][95][96][97] or even templated comments contained within the result report.…”

Una proposta di protocollo per la gestione dell’esame microbiologico delle urine: come garantire l’appropriatezza riducendo il lavoro improduttivo

“…In un recente ed efficace contributo di letteratura in tema di gestione informatica del risultato microbiologico [17], nel mentre gli autori sottolineano che i risultati falsi positivi dovuti a batteriuria asintomatica contribuiscono in modo significativo al management subottimale dei pazienti, suggeriscono altresì di agire migliorando la refertazione, attraverso l'utilizzo di commenti che invitino il clinico a valutare con maggiore attenzione la correlazione tra il risultato microbiologico e il contesto clinico, per evitare trattamenti inappropriati, oppure evitando di refertare i risultati espressione di contaminazione/colonizzazione. Qualunque strada si intenda percorrere, si tratta comunque di una rivoluzione dell'approccio diagnostico, finalmente "olistico", e non più focalizzato al solo risultato biologico dell'esame colturale.…”

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

“…The accelerated obsolescence of the sequencing platforms presents several obstacles in bridging the gap between research and routine diagnostics including standardizations efforts [23]. The downstream bioinformatics pipelines are also unique challenges for the microbiology laboratory both in terms of infrastructure and skilled operators [24–27]. Overall, WGS ‘wet bench-dry bench’ workflow represents an integrated process, which is not easily amenable to the traditional quality metrics used by the microbiology laboratories [27–29].…”