Using fecal immmunochemical cartridges for gut microbiome analysis within a colorectal cancer screening program

ABSTRACT

The colorectal cancer (CRC) screening program B-PREDICT is an invited two-stage screening project using a fecal immunochemical test (FIT) for initial screening followed by a colonoscopy for those with a positive FIT. Since the gut microbiome likely plays a role in the etiology of CRC, microbiome-based biomarkers in combination with FIT could be a promising tool for optimizing CRC screening. Therefore, we evaluated the usability of FIT cartridges for microbiome analysis and compared it to Stool Collection and Preservation Tubes. Corresponding FIT cartridges as well as Stool Collection and Preservation Tubes were collected from participants of the B-PREDICT screening program to perform 16S rRNA gene sequencing. We calculated intraclass correlation coefficients (ICCs) based on center log ratio transformed abundances and used ALDEx2 to test for significantly differential abundant taxa between the two sample types. Additionally, FIT and Stool Collection and Preservation Tube triplicate samples were obtained from volunteers to estimate variance components of microbial abundances. FIT and Preservation Tube samples produce highly similar microbiome profiles which cluster according to subject. Significant differences between the two sample types can be found for abundances of some bacterial taxa (e.g. 33 genera) but are minor compared to the differences between the subjects. Analysis of triplicate samples revealed slightly worse repeatability of results for FIT than for Preservation Tube samples. Our findings indicate that FIT cartridges are appropriate for gut microbiome analysis nested within CRC screening programs.

KEYWORDS:

• Microbiome
• colorectal cancer
• 16S rRNA sequencing
• FIT
• NORGEN

Abbreviations

ASV: Amplicon sequence variants; B-PREDICT: Burgenland Prevention Trial of Colorectal Cancer Disease with Immunological Testing; BMI: Body mass index; CRC: Colorectal cancer; CORSA: Colorectal Cancer Study of Austria; CLR: Centre log ratio; FIT: Fecal immunochemical test; FOBT: Fecal occult blood test; ICC: Intraclass correlation coefficient

Acknowledgments

We kindly thank all individuals who agreed to participate in CORSA. Furthermore, we thank all cooperating physicians and students.

Declarations

Ethical Approval and Consent to participate

Written consent was obtained from all study participants and all studies were approved by the corresponding Institutional Review Board. Compliance with the 1964 Declaration of Helsinki, the Austrian Drug Law (Arzneimittelgesetz, AMG) and the requirements of Good Clinical Practice of the European Community (CPMP/ICH/135/95) will be ensured. The CORSA study was approved by the institutional review boards (EK 33/2010 and EK 1160/2016).

Availability of data and materials

Raw sequencing data and patient metadata are available at the NCBI Sequence

Read Archive (BioProject PRJNA801143).

R-scripts used in the analysis can be found hear: https://github.com/martin-borkovec/corsa-microbiome.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

SB, MB and AG designed and coordinated the study; AG supervised this study. AG together with BS and NG received funding to conduct the study. FB, PG, TG, MH, GL and RL collected samples and coordinated sample recruitment; SB carried out DNA isolation and sample preparation. SB, MB, AB, AF, CJ and AG participated in data analysis and result interpretation; MB prepared figures and tables; SB, MB and AG drafted the manuscript; All authors have read and approved the manuscript.

Preprint

The present manuscript has been uploaded as Author’s Original Manuscript for preprint at https://doi.org/10.21203/rs.3.rs-1294888/v1.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2176119

Additional information

Funding

This study was funded by the “Österreichische Forschungsförderungsgesellschaft” FFG BRIDGE (grant 880626, to Andrea Gsur) and was supported by COST Action CA17118.