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  • Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis

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Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis
  1. Andrea C Masi1,
  2. Yaa E A Oppong2,
  3. Beate Haugk3,
  4. Christopher A Lamb1,4,
  5. Linda Sharp5,
  6. James M Shaw1,
  7. Christopher J Stewart1,
  8. Kofi W Oppong1,6
  1. 1 Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
  2. 2 Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
  3. 3 Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
  4. 4 Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
  5. 5 Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
  6. 6 HPB Unit and Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
  1. Correspondence to Dr Kofi W Oppong, HPB Unit and Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE7 7DN, UK; kofi.oppong{at}nhs.net

http://dx.doi.org/10.1136/gutjnl-2020-322457

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    We read with great interest the study by Gaiser et al 1; their finding of enrichment of oral bacterial taxa, including Fusobacterium nucleatum, in intraductal papillary mucinous neoplasms with high-grade dysplasia adds to the growing literature on the pancreatic microbiome in pancreatic ductal adenocarcinoma (PDAC).2–4 Previous PDAC microbiome studies have an inherent bias as they are restricted to samples from patients undergoing surgical resection. Less than 20% of patients with PDAC undergo surgery and such cases are not representative of the full gamut of the disease. Additionally there is uncertainty regarding the extent of exogenous bacterial DNA contamination of samples used.

    Endoscopic ultrasound (EUS) fine needle biopsy (FNB) is often utilised to make a histological diagnosis in patients with suspected PDAC. Novel needles which provide samples better suited to DNA extraction and gene sequencing5 are available. However, the relatively low biomass of the samples and nature of sample collection present challenges with contamination and technical noise. Recently computational approaches have been developed to remove contaminants in such low …

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    Footnotes

    • ACM and YEAO are joint first authors.

    • CJS and KWO are joint senior authors.

    • Twitter @ACMasi10, @DrChrisLamb

    • Contributors KO, CS, YEAO and CAL designed the study. AM and CS generated the data. YEAO and CS performed bioinformatic and statistical analysis. KO, and CS led the work and wrote the first and last draft of the manuscript. All authors contributed to study design and edited the manuscript. All authors approved the final draft.

    • Funding CS is supported by the NUAcT (Newcastle University Academic Track) scheme.

    • Competing interests KO and BH have received research funding from Medtronic. JMS has received honoraria for participation in Medtronic Scientific Advisory Boards.

    • Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting or dissemination plans of this research.

    • Provenance and peer review Not commissioned; internally peer reviewed.