Centralised or Localised Pathogen Whole Genome Sequencing: Lessons Learnt From Implementation in a Clinical Diagnostic Laboratory.

Frontiers in Cellular and Infection Microbiology
Alicia G BeukersSebastiaan J van Hal

Abstract

Whole genome sequencing (WGS) has had widespread use in the management of microbial outbreaks in a public health setting. Current models encompass sending isolates to a central laboratory for WGS who then produce a report for various levels of government. This model, although beneficial, has multiple shortcomings especially for localised infection control interventions and patient care. One reason for the slow rollout of WGS in clinical diagnostic laboratories has been the requirement for professionally trained personal in both wet lab techniques and in the analysis and interpretation of data, otherwise known as bioinformatics. A further bottleneck has been establishment of regulations in order to certify clinical and technical validity and demonstrate WGS as a verified diagnostic test. Nevertheless, this technology is far superior providing information that would normally require several diagnostic tests to achieve. An obvious barrier to informed outbreak tracking is turnaround time and requires isolates to be sequenced in real-time to rapidly identify chains of transmission. One way this can be achieved is through onsite hospital sequencing with a cumulative analysis approach employed. Onsite, as opposed to centralised sequen...Continue Reading

References

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Aug 8, 2012·Nature Reviews. Genetics·Xavier DidelotDerrick W Crook
Apr 17, 2015·Clinical Microbiology Reviews·Carol A GilchristErik L Hewlett
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Dec 3, 2017·Diagnostic Microbiology and Infectious Disease·Vidthiya MenonSebastiaan J van Hal
Jan 20, 2018·Emerging Infectious Diseases·Rowena McMullanRebecca Davis
Mar 23, 2018·The Journal of Antimicrobial Chemotherapy·Sebastiaan J van HalVitali Sintchenko
May 31, 2018·Antimicrobial Agents and Chemotherapy·Alicia G BeukersSebastiaan J van Hal
Jun 14, 2019·Foodborne Pathogens and Disease·Eric BrownPeter Gerner-Smidt
Feb 6, 2020·The Journal of Antimicrobial Chemotherapy·Alicia G BeukersSebastiaan J van Hal
Dec 11, 2020·Nature Communications·Rowena A BullIra W Deveson

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