Techniques in bacterial strain typing: past, present, and future

Shelby R. Simar, Blake M. Hanson, Cesar A. Arias

Research output: Contribution to journalReview articlepeer-review

13 Scopus citations


PURPOSE of reviewThe advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies.Recent findingsWGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training.SummaryGenomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.

Original languageEnglish (US)
Pages (from-to)339-345
Number of pages7
JournalCurrent opinion in infectious diseases
Issue number4
StatePublished - Aug 1 2021


  • bacteria
  • strain typing
  • surveillance
  • whole-genome sequencing

ASJC Scopus subject areas

  • Medicine(all)


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