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Legionnaires Outbreak in Harlem

53:21 recording · AUTO · 4 speakers

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Brief overview

Automated whole genome sequencing halves strain-typing time, while a recoded 57-codon E. coli shows genome rewriting remains hard.

  1. Automated sequencing saves almost a day per runTurnaround fell from 44 to 47 hours to 28 hours, with hands-on time cut from five hours to two.
  2. Speed and cost gained without losing accuracyAcross 226 clinical isolates the automated platform agreed with Mayo's core genome multi-locus sequence typing at greater than 99%.
  3. Rewriting a genome is slow, stepwise workSyn57 needed 39 recoded strains joined by conjugation, and the finished strain still grows four times more slowly than wild type.
Executive Summary AI
  • Vincent Racaniello opens with a Legionnaires' disease outbreak in Harlem, New York City, with over 60 cases and three deaths, and the panel ties the bacterium to cooling towers and rooftop water tanks and back to the 1976 Legionnaires convention in Philadelphia.2:27
  • Michelle Swanson presents "Automated Whole Genome Sequencing Platform for Bacterial Strain Typing in Clinical Microbiology Laboratories" by Rachel Siddell, Jordan Starkey and Robin Patel of the Mayo Clinic in Rochester, Minnesota, published in the Journal of Clinical Microbiology in May of this year, with Clear Labs of San Carlos, California as both protocol developer and a funder.6:45
  • The Mayo group compared 226 isolates from 18 different species, collected across the country and one set from France, against their own core genome multi-locus sequence typing, and found fidelity between the two systems greater than 99%.15:14
  • Automation cut hands-on time from about five hours to two, total turnaround from about 44 to 47 hours down to 28 hours, and cost by around 34% to 48%, 49% depending on batch size, with up to 12 samples run simultaneously.17:13
  • Petra Levin then covers "Escherichia coli with a 57 codon genetic code" from Jason Chin's lab in Cambridge, UK, where recoded 100-kilobase segments assembled in yeast and moved in one by one produced Syn57, a fully synthetic 4 million base genome that doubles every 80 minutes instead of 20.26:41
Key Quote
“So if you want science, no lies, no disinformation, listen to us.”
— Vincent Racaniello1:59
Key Quote
“even though it's still E. coli, strains do indeed matter.”
— Michael Schmidt13:13
Key Quote
“So you're saving almost a day.”
— Michelle Swanson17:28