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

Journal of Antimicrobial Chemotherapy

Volumn 69, Issue 8, 2014, Pages 2215-2223

  Buelow, Elena ^a   Gonzalez, Teresita Bello ^b   Versluis, Dennis ^b   Oostdijk, Evelien A N ^a   Ogilvie, Lesley A ^c,d   van Mourik, Maaike S M ^a   Oosterink, Els ^a   van Passel, Mark W J ^b   Smidt, Hauke ^b   D'Andrea, Marco Maria ^e   de Been, Mark ^a   Jones, Brian V ^c,f   Willems, Rob J L ^a   Bonten, Marc J M ^a   van Schaik, Willem ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF BRIGHTON   (United Kingdom)

^d MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^e UNIVERSITY OF SIENA   (Italy)

^f QUEEN VICTORIA HOSPITAL   (United Kingdom)

Author keywords

Antibiotic resistance; Intensive care medicine; Metagenomics

Indexed keywords

AMINOGLYCOSIDE; AMPICILLIN; ANTIBIOTIC AGENT; CEFAZOLIN; CEFOTAXIME; COLISTIN; ERYTHROMYCIN; RNA 16S; TETRACYCLINE; TOBRAMYCIN; AMINOGLYCOSIDE 2''-PHOSPHOTRANSFERASE; ANTIINFECTIVE AGENT; BACTERIAL DNA; PHOSPHOTRANSFERASE;

ANTIBIOTIC RESISTANCE; ARTICLE; CLINICAL ARTICLE; CRITICALLY ILL PATIENT; FECES ANALYSIS; GUT RESISTOME; HOSPITAL DISCHARGE; HOSPITALIZATION; HUMAN; INFECTION PREVENTION; INTENSIVE CARE UNIT; INTESTINE; INTESTINE FLORA; LONGITUDINAL STUDY; METAGENOMICS; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SELECTIVE DIGESTIVE DECONTAMINATION; STOMACH EMPTYING; BACTERIUM IDENTIFICATION; CASE REPORT; CLOSTRIDIUM; DNA SEQUENCE; DRUG EFFECTS; FECES; GENETICS; INTENSIVE CARE; ISOLATION AND PURIFICATION; MALE; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OROPHARYNX; PROCEDURES; SYMBIOSIS; WASTE MANAGEMENT;

ANTI-BACTERIAL AGENTS; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; CLOSTRIDIUM; CRITICAL CARE; DECONTAMINATION; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; FECES; HUMANS; INTESTINES; MALE; MICROBIOTA; MOLECULAR SEQUENCE DATA; OROPHARYNX; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

EID: 84904565544     PISSN: 03057453     EISSN: 14602091     Source Type: Journal    
DOI: 10.1093/jac/dku092     Document Type: Article

References (34)

1. Vincent JL, Rello J, Marshall J et al. International study of the prevalence and outcomes of infection in intensive care units. JAMA 2009; 302: 2323-9.
2. Cosgrove SE. The relationship between antimicrobial resistance and patient outcomes: mortality, length of hospital stay, and health care costs. Clin Infect Dis 2006; 42 Suppl 2: S82-9.
3. de Smet AM, Kluytmans JA, Cooper BS et al. Decontamination of the digestive tract and oropharynx in ICU patients. N Engl J Med 2009; 360: 20-31.
4. de Jonge E, Schultz MJ, Spanjaard L et al. Effects of selective decontamination of digestive tract on mortality and acquisition of resistant bacteria in intensive care: a randomised controlled trial. Lancet 2003; 362: 1011-6.
5. van der Waaij D, Manson WL, Arends JP et al. Clinical use of selective decontamination: the concept. Intensive Care Med 1990; 16 Suppl 3: S212-6.
6. van der Meer JW, Vandenbroucke-Grauls CM. Resistance to selective decontamination: the jury is still out. Lancet Infect Dis 2013; 13: 282-3.
7. DanemanN, Sarwar S, Fowler RA et al. Effect of selective decontamination on antimicrobial resistance in intensive care units: a systematic review and meta-analysis. Lancet Infect Dis 2013; 13: 328-41.
8. Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
9. Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009; 325: 1128-31.
10. Shoemaker NB, Vlamakis H, Hayes K et al. Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl Environ Microbiol 2001; 67: 561-8.
11. Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 2007; 4: 55-61.
12. Ogilvie LA, Bowler LD, Caplin J et al. Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. Nat Commun 2013; 4: 2420.
13. Rajilic-Stojanovic M, Heilig HG, Molenaar D et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 2009; 11: 1736-51.
14. Qin J, Li Y, Cai Z et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012; 490: 55-60.
15. Altschul SF, Madden TL, Schaffer AA et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-402.
16. Fu L, Niu B, Zhu Z et al. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28: 3150-2.
17. GerlachW, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 2011; 39: e91.
18. Hemmerich C, Buechlein A, Podicheti R et al. An Ergatis-based prokaryotic genome annotation web server. Bioinformatics 2010; 26: 1122-4.
19. Leplae R, Lima-Mendez G, Toussaint A. ACLAME: A CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 2010; 38: D57-61.
20. Siguier P, Perochon J, Lestrade L et al. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34: D32-6.
21. Salonen A, Nikkila J, Jalanka-Tuovinen J et al. Comparative analysis of faecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 2010; 81: 127-34.
22. Gloor GB, Hummelen R, Macklaim JM et al. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 2010; 5: e15406.
23. van den Bogert B, de Vos WM, Zoetendal EG et al. Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 2011; 77: 2071-80.
24. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 22DDCT method. Methods 2001; 25: 402-8.
25. Rajilic-Stojanovic M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007; 9: 2125-36.
26. Ubeda C, Taur Y, Jenq RR et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 2010; 120: 4332-41.
27. Forslund K, Sunagawa S, Kultima JR et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res 2013; 23: 1163-9.
28. Hu Y, Yang X, Qin J et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 2013; 4: 2151.
29. Oostdijk EA, de Smet AM, Blok HE et al. Ecological effects of selective decontamination on resistant Gram-negative bacterial colonization. Am J Respir Crit Care Med 2010; 181: 452-7.
30. Holmstrom K, Collins MD, Moller T et al. Subdoligranulum variabile gen. nov., sp. nov. from human faeces. Anaerobe 2004; 10: 197-203.
31. Bryan LE, Kowand SK, Van Den Elzen HM. Mechanismof aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis. Antimicrob Agents Chemother 1979; 15: 7-13.
32. Janvilisri T, Scaria J, Gleed R et al. Development of a microarray for identification of pathogenic Clostridium spp. Diagn Microbiol Infect Dis 2010; 66: 140-7.
33. Jones BV, Sun F, Marchesi JR. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC Genomics 2010; 11: 46.
34. Chow JW, Kak V, You I et al. Aminoglycoside resistance genes aph(2″)-Ib and aac(6′)-Im detected together in strains of both Escherichia coli and Enterococcus faecium. Antimicrob Agents Chemother 2001; 45: 2691-4.