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Review
. 2020 Dec;40(4):447-458.
doi: 10.1016/j.cll.2020.08.003. Epub 2020 Oct 1.

Clinical Pathogen Genomics

Andrew Cameron  1 , Jessica L Bohrhunter  1 , Samantha Taffner  1 , Adel Malek  2 , Nicole D Pecora  3
Affiliations
Review

Clinical Pathogen Genomics

Andrew Cameron et al. Clin Lab Med. 2020 Dec.

Abstract

Recent improvements in next-generation sequencing technologies have enabled clinical laboratories to increasingly pursue pathogen genomics for infectious disease diagnosis. Clinical laboratories can also benefit from whole-genome sequence characterization of cultured isolates, helping to resolve infection prevention questions pertaining to pathogen outbreaks and surveillance. Metagenomic sequencing from primary specimens can also provide laboratories with an unbiased universal test for situations where traditional methods fail to identify infectious etiologies despite, high clinical suspicion. Here, the most useful applications of whole-genome sequence and metagenomic sequencing are summarized, as are the main advantages, limitations, and considerations for building an in-house clinical genomics program.

Keywords: Clinical metagenomics; Clinical pathogen genomics; Next-generation sequencing; Pathogen whole-genome sequencing.

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Conflict of interest statement

Disclosure No author has commercial or financial conflicts of interest. N.D. Pecora is supported by funds available from the Department of Pathology and Laboratory Medicine, University of Rochester Medical Center.

Figures

Fig. 1
Fig. 1
Integration of Pathogen Genomics into the Clinical Microbiology Laboratory. MLST, multilocus sequence typing; QC, quality control; SNP, single nucleotide polymorphism.
See this image and copyright information in PMC

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