Evaluation of whole-genome enrichment and sequencing of T. pallidum from FFPE samples after 75 years

Summary

The recent developments in genomic sequencing have permitted the publication of many new complete genome sequences of Treponema pallidum pallidum, the bacterium responsible for syphilis, which has led to a new understanding of its phylogeny and diversity. However, few archived samples are available, because of the degradability of the bacterium and the difficulties in preservation.

We present a complete genome obtained from a Formalin-Fixed Paraffin-Embedded (FFPE) organ sample from 1947, kept at the Strasbourg Faculty of Medicine. This is the preliminary, proof-of concept study of this collection/biobank of more than 1.5 million FFPE samples and the evaluation of the feasibility of genomic analyses.

We demonstrate here that even degraded DNA from fragile bacteria can be recovered from 75-year-old FFPE samples and therefore propose that such collections as this one can function as sources of biological material for genetic studies of pathogens, cancer, or even the historical human population itself.

Graphical abstract

Highlights

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  FFPE samples can still be used for genomic studies 75 years after embedding

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  Whole-genome enrichment can be successful even with fragile degraded bacteria

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  A new avenue of research into symptom-strain correlation in diseases like syphilis

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  Archived FFPE samples and medical records constitute potential biobanks of samples

Abstract

Medical microbiology; Medical biotechnology