The effect of selective decontamination on the intestinal microbiota as measured with IS-pro: a taxonomic classification tool applicable for direct evaluation of intestinal microbiota in clinical routine

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Abstract

Selective decontamination of the digestive tract (SDD) is aimed at elimination of potential pathogenic microorganisms. In this study, the effect of SDD on gut microbiota was evaluated in a large homogenous group of elective colorectal cancer surgery patients. Rectal swabs were taken from 118 patients undergoing colorectal surgery. These patients were randomly assigned to receive perioperative SDD or to the control group (no SDD). Rectal swabs were taken prior to surgery, 3 days after commencing administration of SDD. Gut microbial profiles were obtained with the IS-pro technique, a standardized microbiota profiling assay applicable in clinical routine. Differences in abundance for different taxonomical groups and diversity between the groups were assessed. Unsupervised and supervised classification techniques were used to assess microbial signatures, differentiating between the SDD group and the control group. Patients in the SDD group had different gut microbial signatures than in the control group, also in phyla that are not a target for SDD. Escherichia coli, Sutterella spp., Faecalibacterium prausnitzii, and Streptococcus spp. were the species that differed the most between the two groups. The SDD group showed clustering into two subgroups. In one subgroup, a decrease in Proteobacteria was observed, whereas the other subgroup showed a shift in Proteobacteria species. This study shows that SDD not only decreases colonization of the gastrointestinal tract with potential pathogenic Gram-negative microorganisms, but also reduces the abundance of normal colonizers of our gastrointestinal system and leads to a shift in total microbiota composition.

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Author and article information

Contributors

M. L. M. van Doorn-Schepens: m.l.m.vandoornschepens@olvg.nl

Journal

Journal ID (nlm-ta): Eur J Clin Microbiol Infect Dis

Journal ID (iso-abbrev): Eur J Clin Microbiol Infect Dis

Title: European Journal of Clinical Microbiology & Infectious Diseases

Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )

ISSN (Print): 0934-9723

ISSN (Electronic): 1435-4373

Publication date (Electronic): 1 October 2022

Publication date PMC-release: 1 October 2022

Publication date (Print): 2022

Volume: 41

Issue: 11

Pages: 1337-1345

Affiliations

[1 ]GRID grid.12380.38, ISNI 0000 0004 1754 9227, Department of Medical Microbiology and Infection Control, , Amsterdam UMC, Vrije Universiteit Amsterdam, ; De Boelelaan 1118, PK1X124, Amsterdam, 1081 HZ the Netherlands

[2 ]GRID grid.440209.b, ISNI 0000 0004 0501 8269, Laboratory of Medical Microbiology, , Onze Lieve Vrouwe Gasthuis, ; Amsterdam, the Netherlands

[3 ]GRID grid.12380.38, ISNI 0000 0004 1754 9227, Department of Surgery, Amsterdam UMC, , Vrije Universiteit Amsterdam, ; Amsterdam, the Netherlands

[4 ]GRID grid.414725.1, ISNI 0000 0004 0368 8146, Department of Surgery, , Meander Medical Center, ; Amersfoort, the Netherlands

[5 ]GRID grid.416219.9, ISNI 0000 0004 0568 6419, Department of Surgery, , Spaarne Gasthuis Hospital, ; Haarlem/Hoofddorp, The Netherlands

[6 ]GRID grid.12380.38, ISNI 0000 0004 1754 9227, Department of Molecular Cell Biology and Immunology, , Amsterdam UMC, Vrije Universiteit Amsterdam, ; Amsterdam, the Netherlands

[7 ]Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands

[8 ]In Biome, Science Park, 116, Amsterdam, 1081 XG The Netherlands

[9 ]GRID grid.412966.e, ISNI 0000 0004 0480 1382, Department of Medical Microbiology, , NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, ; Maastricht, The Netherlands

Article

Publisher ID: 4483

DOI: 10.1007/s10096-022-04483-8

PMC ID: 9556388

PubMed ID: 36181564

SO-VID: 3efadaa0-d8ed-4569-ae56-7977edd6487b

License:

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