Impact of Digestive and Oropharyngeal decontamination on the Intestinal Microbiota in ICU Patients

Robin F Benus 1,2,3, Hermie J Harmsen 1, Gjalt W Welling 1, Rob Spanjersberg 2, Jan G Zijlstra 2, John E Degener 1, and Tjip S van der Werf 3

Departments of 1 Medical Microbiology, 2 Critical Care, and 3 Internal Medicine, and Pulmonary Diseases & Tuberculosis, Infectious Diseases & Tuberculosis Service; University Medical Centre Groningen, University of Groningen, the Netherlands

Correspondence:

Dr TS van der Werf,

Hanzeplein 1, POBox 30001, AA11, room U3.105, 9700RB Groningen

Tel. +31 50 3611501 Fax +31 50 3619320

Supplemental Data:

Target / Probe/stain / Sequence / reference
Total bacteria / EUB338 / 5’GCTGCCTCCCGTAGGAGT / Amann [1]
Bacteroides / Prevotella / Bac303 / 5’CCAATGTGGGGGACCTT / Manz [2]
E. rectale / Blautia coccoides / Erec482 / 5’GCTTCTTAGTCA(G/A)GTACCG / Franks [3]
F. prausnitzii-group / Fprau645 / 5’CCTCTGCACTACTCAAGAAAAAC / Suau [4]
Atopobium-group / Ato291 / 5’GGTCGGTCTCTCAACCC / Harmsen [5]
Bifidobacteria / Bif164 / 5’CATCCGGCATTACCACCC / Langendijk [6]
Ruminococci / Rbro730
Rfla729 / 5’TAAAGCCCAGYAGGCCGC
5’AAAGCCCAGTAAGCCGCC / Harmsen [7]
Roseburia cluster / Rint623 / 5’TTCCAATGCAGTACCGGG / Hold [8]
Rint helper / 5’GTTGAGCCCCGGGCTTT / Aminov [9]
Enterobacteriaceae / EC1531 / 5’CACCGTAGTGCCTCGTCATCA / Poulsen [10]
Enterococcus faecalis / Enfl84 / 5’CCTCTTTCCAATTGAGTGCA / Waar [11]
Enterococcus faecium-group / Enfm93 / 5’GCCACTCCTCTTTTTCCGG / Waar [11]

References

1. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 1990;56:1919-1925.

2. Manz W, Amann R, Ludwig W, Vancanneyt M, Schleifer KH. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 1996;142 ( Pt 5):1097-1106.

3. Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 1998;64:3336-3345.

4. Suau A, Rochet V, Sghir A et al. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst Appl Microbiol 2001;24:139-145.

5. Harmsen HJ, Wildeboer-Veloo AC, Grijpstra J, Knol J, Degener JE, Welling GW. Development of 16S rRNA-based probes for the Coriobacterium group and the Atopobium cluster and their application for enumeration of Coriobacteriaceae in human feces from volunteers of different age groups. Appl Environ Microbiol 2000;66:4523-4527.

6. Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, Welling GW. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol 1995;61:3069-3075.

7. Harmsen HJ, Raangs GC, He T, Degener JE, Welling GW. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 2002;68:2982-2990.

8. Hold GL, Schwiertz A, Aminov RI, Blaut M, Flint HJ. Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces. Appl Environ Microbiol 2003;69:4320-4324.

9. Aminov RI, Walker AW, Duncan SH, Harmsen HJ, Welling GW, Flint HJ. Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Appl Environ Microbiol 2006;72:6371-6376.

10. Poulsen LK, Lan F, Kristensen CS, Hobolth P, Molin S, Krogfelt KA. Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization. Infect Immun 1994;62:5191-5194.

11. Waar K, Degener JE, van Luyn MJ, Harmsen HJ. Fluorescent in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples. J Med Microbiol 2005;54:937-944.