Effects of selective digestive decontamination (SDD) on the gut resistome

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Effects of selective digestive decontamination (SDD) on the gut resistome. / Buelow, Elena; Gonzalez, Teresita Bello; Versluis, Dennis; Oostdijk, Evelien A N; Ogilvie, Lesley A; van Mourik, Maaike S M; Oosterink, Els; van Passel, Mark W J; Smidt, Hauke; D'Andrea, Marco Maria; de Been, Mark; Jones, Brian V; Willems, Rob J L; Bonten, Marc J M; van Schaik, Willem.

In: Journal of Antimicrobial Chemotherapy, Vol. 69, No. 8, 01.08.2014, p. 2215-23.

Research output: Contribution to journalArticlepeer-review

Harvard

Buelow, E, Gonzalez, TB, Versluis, D, Oostdijk, EAN, Ogilvie, LA, van Mourik, MSM, Oosterink, E, van Passel, MWJ, Smidt, H, D'Andrea, MM, de Been, M, Jones, BV, Willems, RJL, Bonten, MJM & van Schaik, W 2014, 'Effects of selective digestive decontamination (SDD) on the gut resistome', Journal of Antimicrobial Chemotherapy, vol. 69, no. 8, pp. 2215-23. https://doi.org/10.1093/jac/dku092

APA

Buelow, E., Gonzalez, T. B., Versluis, D., Oostdijk, E. A. N., Ogilvie, L. A., van Mourik, M. S. M., Oosterink, E., van Passel, M. W. J., Smidt, H., D'Andrea, M. M., de Been, M., Jones, B. V., Willems, R. J. L., Bonten, M. J. M., & van Schaik, W. (2014). Effects of selective digestive decontamination (SDD) on the gut resistome. Journal of Antimicrobial Chemotherapy, 69(8), 2215-23. https://doi.org/10.1093/jac/dku092

Vancouver

Buelow E, Gonzalez TB, Versluis D, Oostdijk EAN, Ogilvie LA, van Mourik MSM et al. Effects of selective digestive decontamination (SDD) on the gut resistome. Journal of Antimicrobial Chemotherapy. 2014 Aug 1;69(8):2215-23. https://doi.org/10.1093/jac/dku092

Author

Buelow, Elena ; Gonzalez, Teresita Bello ; Versluis, Dennis ; Oostdijk, Evelien A N ; Ogilvie, Lesley A ; van Mourik, Maaike S M ; Oosterink, Els ; van Passel, Mark W J ; Smidt, Hauke ; D'Andrea, Marco Maria ; de Been, Mark ; Jones, Brian V ; Willems, Rob J L ; Bonten, Marc J M ; van Schaik, Willem. / Effects of selective digestive decontamination (SDD) on the gut resistome. In: Journal of Antimicrobial Chemotherapy. 2014 ; Vol. 69, No. 8. pp. 2215-23.

Bibtex

@article{b1757caada704935af56a76849be672f,
title = "Effects of selective digestive decontamination (SDD) on the gut resistome",
abstract = "OBJECTIVES: Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches.METHODS: We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD.RESULTS: The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2″)-Ib and an aadE-like gene. We show that aph(2″)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ∼10(4) fold increase to a ∼10(-10) fold decrease in relative abundance during SDD.CONCLUSIONS: ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.",
keywords = "Anti-Bacterial Agents, Bacterial Typing Techniques, Base Sequence, Clostridium, Critical Care, DNA, Bacterial, Decontamination, Drug Resistance, Bacterial, Feces, Humans, Intestines, Male, Microbiota, Molecular Sequence Data, Oropharynx, Phosphotransferases (Alcohol Group Acceptor), RNA, Ribosomal, 16S, Sequence Analysis, DNA, Symbiosis, Case Reports, Journal Article, Research Support, Non-U.S. Gov't",
author = "Elena Buelow and Gonzalez, {Teresita Bello} and Dennis Versluis and Oostdijk, {Evelien A N} and Ogilvie, {Lesley A} and {van Mourik}, {Maaike S M} and Els Oosterink and {van Passel}, {Mark W J} and Hauke Smidt and D'Andrea, {Marco Maria} and {de Been}, Mark and Jones, {Brian V} and Willems, {Rob J L} and Bonten, {Marc J M} and {van Schaik}, Willem",
note = "{\textcopyright} The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.",
year = "2014",
month = aug,
day = "1",
doi = "10.1093/jac/dku092",
language = "English",
volume = "69",
pages = "2215--23",
journal = "Journal of Antimicrobial Chemotherapy",
issn = "0305-7453",
publisher = "Oxford University Press",
number = "8",

}

RIS

TY - JOUR

T1 - Effects of selective digestive decontamination (SDD) on the gut resistome

AU - Buelow, Elena

AU - Gonzalez, Teresita Bello

AU - Versluis, Dennis

AU - Oostdijk, Evelien A N

AU - Ogilvie, Lesley A

AU - van Mourik, Maaike S M

AU - Oosterink, Els

AU - van Passel, Mark W J

AU - Smidt, Hauke

AU - D'Andrea, Marco Maria

AU - de Been, Mark

AU - Jones, Brian V

AU - Willems, Rob J L

AU - Bonten, Marc J M

AU - van Schaik, Willem

N1 - © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PY - 2014/8/1

Y1 - 2014/8/1

N2 - OBJECTIVES: Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches.METHODS: We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD.RESULTS: The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2″)-Ib and an aadE-like gene. We show that aph(2″)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ∼10(4) fold increase to a ∼10(-10) fold decrease in relative abundance during SDD.CONCLUSIONS: ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.

AB - OBJECTIVES: Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches.METHODS: We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD.RESULTS: The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2″)-Ib and an aadE-like gene. We show that aph(2″)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ∼10(4) fold increase to a ∼10(-10) fold decrease in relative abundance during SDD.CONCLUSIONS: ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.

KW - Anti-Bacterial Agents

KW - Bacterial Typing Techniques

KW - Base Sequence

KW - Clostridium

KW - Critical Care

KW - DNA, Bacterial

KW - Decontamination

KW - Drug Resistance, Bacterial

KW - Feces

KW - Humans

KW - Intestines

KW - Male

KW - Microbiota

KW - Molecular Sequence Data

KW - Oropharynx

KW - Phosphotransferases (Alcohol Group Acceptor)

KW - RNA, Ribosomal, 16S

KW - Sequence Analysis, DNA

KW - Symbiosis

KW - Case Reports

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1093/jac/dku092

DO - 10.1093/jac/dku092

M3 - Article

C2 - 24710024

VL - 69

SP - 2215

EP - 2223

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

IS - 8

ER -