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

Buelow, Elena; González, Teresita Bello; Versluis, Dennis; Oostdijk, Evelien; Ogilvie, Lesley A.; Mourik, Maaike S. M. van; Oosterink, Els; Passel, Mark W. J. van; Smidt, Hauke; D’Andrea, Marco Maria; Been, Mark de; Jones, Brian V.; Willems, Rob J. L.; Bonten, Marc J. M.; Schaik, Willem van

doi:10.1093/jac/dku092

Cited by 90 publications

(98 citation statements)

References 32 publications

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“…These findings expand on previous findings of selection of Grampositive cocci (Daneman et al, 2013;Buelow et al, 2014;van der Bij et al, 2016) and depletion of F. prausnitzii during SDD (Benus et al, 2010). In addition, we were able to demonstrate that the abundance of E. coli was reduced by 301-fold (median) during ICU-stay.…”

Section: Discussionsupporting

confidence: 90%

“…Yet, the original claim that these interventions do not affect harmless anaerobic intestinal bacteria (van der Waaij et al, 1990), has recently been questioned (Buelow et al, 2014;Benus et al, 2010). While culture-based studies did not demonstrate selection for antibiotic-resistant opportunistic pathogens during SDD-treatment (de Smet et al, 2009;Daneman et al,2013;Plantinga et al, 2015), concerns remain that selection for antibiotic resistance genes occurs in the gut microbiota of patients.…”

Section: Discussionmentioning

confidence: 99%

“…in showing that tetracycline and aminoglycoside resistance genes and bacteroidal β-lactamases are widespread in the human intestinal microbiota (Sommer et al, 2009;de Vries et al;Forslund et al, 2013;Hu et al, 2013;Buelow et al, 2014). All resistance genes that increased in abundance during ICU-stay, were associated with Previous studies on the implementation of SDD in ICUs have not found evidence for increased rates of MRSA colonization or infection (Daneman et al, 2013;Plantinga et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…During ICU stay, the gut resistome of patients is primarily monitored by the cultivation of resistant bacteria from rectal swabs or faeces, as part of routine diagnostics. However, methods that rely on microbial culture capture only a fraction of the gut resistome, since anaerobic gut commensals, which are the main reservoir of ARGs in the gut microbiota, are difficult to culture (Sommer et al, 2009;, Qin et al, 2010;Buelow et al, 2014). Thus, culture-independent methods need to be employed to assess the impact of topical antibiotic prophylaxis on the microbiota and resistome of ICU patients.…”

Section: Introductionmentioning

confidence: 99%

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Interplay between gut microbiota and antibiotics

Gonzalez¹

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The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria.Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them.The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence.Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype.In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated.Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3'phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosylhydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of nonhuman primates, the applicability of Human Intesti...

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Interplay between gut microbiota and antibiotics

Gonzalez¹

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“…Elle porte à ce jour essentiellement sur le milieu digestif, aboutissant aux conclusions que l'exposition massive à des antibiotiques, que ce soit via leur utilisation dans l'industrie agro-alimentaire [3] ou pour la décontamination digestive sélective des patients de réanimation [4], transforme la flore digestive en un véritable réservoir de gènes de résis-tance aux antibiotiques. Seules deux revues de la littérature abordent ce sujet dans le poumon, dont une publiée dans The Lancet en août 2014 [5].…”

Section: Le Résistome Dans Les Microbiomes Humainsunclassified