RT Journal Article
SR Electronic
T1 Gut microbiota and resistome dynamics in intensive care patients receiving selective digestive tract decontamination
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 102467
DO 10.1101/102467
A1 Elena Buelow
A1 Teresita de Jesús Bello González
A1 Susana Fuentes
A1 Wouter A.A. de Steenhuijsen Piters
A1 Leo Lahti
A1 Jumamurat R. Bayjanov
A1 Eline A.M. Majoor
A1 Johanna C. Braat
A1 Maaike S. M. van Mourik
A1 Evelien A.N. Oostdijk
A1 Rob J.L. Willems
A1 Marc. J.M. Bonten
A1 Mark W.J. van Passel
A1 Hauke Smidt
A1 Willem van Schaik
YR 2017
UL http://biorxiv.org/content/early/2017/01/25/102467.abstract
AB Background Critically ill patients hospitalized in an Intensive Care Unit (ICU) are at increased risk of acquiring potentially life-threatening infections with opportunistic pathogens. The gut microbiota of ICU patients forms an important reservoir for these infectious agents. To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed ‘Selective decontamination of the digestive tract’ (SDD), may be used. SDD has previously been shown to improve clinical outcome in ICU patients, but the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes (‘the resistome’) of ICU patients during SDD.Results During ICU-stay, 30 fecal samples of ten patients were collected. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. As a control group, feces from ten healthy subjects were collected twice, with a one-year interval. Gut microbiota and resistome composition were determined using 16S rRNA phylogenetic profiling and nanolitre-scale quantitative PCRs.The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by low microbial diversity, decreased levels of E. coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6′)-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants and tetracyclines respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects.Conclusions The microbiota and resistome of ICU patients and healthy subjects were noticeably different, but importantly, levels of E. coli remained low during ICU hospitalization, presumably due to SDD therapy. Selection for four antibiotic resistance genes was observed, but none of these are of particular concern as they do not contribute to clinically relevant resistance. Our data support the ecological safety of SDD, at least in settings with low levels of circulating antibiotic resistance.