High-throughput sequencing and clinical microbiology: Progress, opportunities and challenges

Mark J. Pallen*, Nicholas J. Loman, Charles W. Penn

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

104 Citations (Scopus)


High-throughput sequencing is sweeping through clinical microbiology, transforming our discipline in its wake. It is already providing an enhanced view of pathogen biology through rapid and inexpensive whole-genome sequencing and more sophisticated applications such as RNA-seq. It also promises to deliver high-resolution genomic epidemiology as the ultimate typing method for bacteria. However, the most revolutionary effect of this 'disruptive technology' is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming 'technological singularity' in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.

Original languageEnglish
Pages (from-to)625-631
Number of pages7
JournalCurrent Opinion in Microbiology
Issue number5
Publication statusPublished - Oct 2010
Externally publishedYes

Bibliographical note

Funding Information:
We thank the British Biotechnology and Biological Science Research Council for supporting NLJ via grant BBE0111791 and the Hospital Infection Society for supporting the study by Lewis et al.


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