1. Proposed informatics pipeline for microbial genomic analysis in the clinical microbiology laboratory.
Proposed informatics pipeline for microbial genomic analysis in the clinical microbiology laboratory. The clinical purposes of genomic sequencing can be varied, and multiple parallel pipelines and their associated expert systems can be used to analyze data depending on which endpoints are desired. One goal of the microbiology laboratory is to unite the information obtained from these various pipelines into a clinically relevant and concise report that can guide patient care. A second goal is to characterize a potential agent of an emerging outbreak so that future samples can be monitored for this agent of interest. The genomic characterization of this outbreak agent can be shared with public health agencies, which can also alert other laboratories to monitor their samples for this emerging agent. Solid arrows show the flow of analysis. Dotted arrows show the transfer of information about outbreak agents into expert system knowledge databases. Wet laboratory analysis is shown in red, and dry laboratory analysis is shown in blue. Information available to clinicians is shown in yellow. Asterisks mark data that may be appropriate for long-term storage.
Daniel D. Rhoads et al. Clin. Microbiol. Rev. 2014; doi: /CMR