Biology subjects

Bonten, M. J. M.

Publications and source records attributed to Bonten, M. J. M..

8 recordsLinked to original sources

bioRxiv2018

Bariatric surgery changes gut microbiota composition independent of operation type

BackgroundBariatric surgery in patients with morbid obesity, either through gastric sleeve gastrectomy or Roux-Y gastric bypass surgery, leads to sustainable weight loss, improvement of metabolic disorders and changes in the intestinal microbiota. Yet, the relationship between changes in gut microbiota, weight loss and the surgical procedure remains incompletely understood.\n\nSubjects/MethodsWe determined temporal changes in microbiota composition in 45 obese patients undergoing a crash diet followed by gastric sleeve gastrectomy (n= 22) or Roux-Y gastric bypass (n= 23). Intestinal microbiota composition was determined before intervention (baseline, S1), 2 weeks after a crash diet (S2), and 1 week (S3), 3 months (S4) and 6 months (S5) after surgery.\n\nResultsRelative to S1, the microbial diversity index declined at S2 and S3 (p< 0.05), and gradually returned to baseline levels at S5. The crash diet was associated with an increased abundance of Rikenellaceae and decreased abundances of Ruminococcaceae and Streptococcaceae (p< 0.05). After surgery, at S3, the relative abundance of Bifidobacteriaceae had decreased (compared to the moment directly after the crash diet), whereas those of Streptococcaceae and Enterobacteriaceae had increased (p< 0.05). Increased weight loss during the next 6 months was not associated without major changes in microbiota composition. Significant differences between both surgical procedures were not observed at any of the time points.\n\nConclusionsIn conclusion, undergoing a crash diet and bariatric surgery were associated with an immediate but temporary decline in the microbial diversity, with immediate and permanent changes in microbiota composition, with no differences between patients undergoing gastric sleeve gastrectomy or Roux-Y gastric bypass surgery.

microbiology↗

bioRxiv2017

The microbiome and resistome of hospital sewage during passage through the community sewer system

Effluents from wastewater treatment plants (WWTPs) have been proposed to act as point sources of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) in the environment. Hospital sewage may contribute to the spread of ARB and ARGs as it contains the feces and urine of hospitalized patients, who are more frequently colonized with multi-drug resistant bacteria than the general population. However, whether hospital sewage noticeably contributes to the quantity and diversity of ARGs in the general sewerage system has not yet been determined.\n\nHere, we employed culture-independent techniques, namely 16S rRNA and nanolitre-scale quantitative PCRs, to describe the role of hospital effluent as a point source of ARGs in the sewer system, through comparing microbiota composition and levels of ARGs in hospital sewage with WWTP influent, WWTP effluent and the surface water in which the effluent is released.\n\nCompared to other sample sites, hospital sewage was richest in human-associated bacteria and contained the highest relative levels of ARGs. Yet, the abundance of ARGs was comparable in WWTPs with and without hospital wastewater, suggesting that hospitals do not contribute to the spread of ARGs in countries with a functioning sewerage system.

microbiology↗

bioRxiv2017

Myocardial injury in critically ill patients with community-acquired pneumonia

BackgroundMyocardial injury, as reflected by elevated cardiac troponin levels in plasma, is common in patients with community-acquired pneumonia (CAP), but its temporal dynamics and etiology remain unknown. Our aim was to determine the incidence of troponin release in patients with CAP and identify risk factors which may point to underlying etiologic mechanisms.\n\nMethodsWe included consecutive patients admitted with severe CAP to two intensive care units in the Netherlands between 2011 and 2015. High-sensitivity cardiac troponin I was measured daily during the first week. We used multivariable linear regression to identify variables associated with troponin release on admission, and mixed-effects regression to model the daily rise and fall of troponin levels over time.\n\nResultsAmong 200 eligible patients, 179 were included, yielding 792 observation days. A total of 152 (85%) patients developed raised troponin levels >26 ng/L. Baseline factors independently associated with troponin release included coronary artery disease (160% increase, 95% CI 7-529), smoking (304% increase, 95% CI 59-924), and higher APACHE IV score (2% increase, 95% CI 0.7-3.3), whereas Staphylococcus aureus as a causative pathogen was protective (67% reduction, 95% CI 9-88). Time-dependent risk factors independently associated with daily increase in troponin concentrations included reduced platelet count (1.7% increase, 95% CI 0.1-3.4), tachycardia (1.6% increase, 95% CI 0.3-3), hypotension (5.1% increase, 95% CI 1-9.4) and dobutamine use (38.4% increase 95% CI 8.8-76).\n\nConclusionsCardiac injury develops in a majority of patients with severe CAP. Myocardial oxygen supply-demand mismatch and activated coagulation are potential causes of this injury.

epidemiology↗

bioRxiv2017

Diagnostic Prediction Tools For Bacteraemia Caused By 3rd Generation Cephalosporin-Resistant Enterobacteriaceae In Suspected Bacterial Infections: A Nested Case-Control Study

ObjectivesCurrent guidelines for empirical antibiotic treatment poorly predict the presence of 3rd generation cephalosporin resistant Enterobacteriaceae (3GC-R EB) as a cause of infection, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems to better predict the presence of 3GC-R EB as a cause of bacteraemia.\n\nMethodsA retrospective nested case-control study was performed that included patients [≥]18 years in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GC-R EB bacteraemia was matched to four control infection episodes within the same hospital, based on blood culture date and onset location (community or hospital). Starting from 32 described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GC-R EB bacteraemia.\n\nResults3GC-R EB bacteraemia occurred in 90 of 22,506 (0.4%) community-onset and in 82 of 8,110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes, respectively. The derived community-onset and hospital-onset scoring system consisted of 6 and 9 predictors, respectively, with c-statistics of 0.807 (95% confidence interval 0.756-0.855) and 0.842 (0.794-0.887). With selected score cutoffs, the models identified 3GC-R EB bacteraemia with equal sensitivity as existing guidelines, but reduced the proportion of patients classified as at risk for 3GC-R EB bacteraemia (i.e. eligible for empiric carbapenem therapy) with 40% in patients with community-onset and 49% in patients with hospital-onset infection.\n\nConclusionsThese prediction rules for 3GC-R EB bacteraemia may reduce unnecessary empiric carbapenem use.

epidemiology↗

bioRxiv2017

Cardiac events after macrolides or fluoroquinolones in patients hospitalized for community-acquired pneumonia: post-hoc analysis of a cluster-randomized trial

BackgroundGuidelines recommend macrolides and fluoroquinolones in patients hospitalized with community-acquired pneumonia (CAP), but their use has been associated with cardiac events.\n\nObjectiveTo quantify associations between macrolide and fluoroquinolone use and cardiac events in patients hospitalized with CAP in non-ICU wards.\n\nDesignPost-hoc analysis of a cluster-randomized trial\n\nSettingSix hospitals in the Netherlands\n\nPatientsCAP patients admitted to non-ICU wards and without a cardiac event on admission\n\nMeasurementsCause-specific hazard ratios (HRs) were calculated for effects of time-dependent macrolide and fluoroquinolone exposure on cardiac events, defined as occurrence of new or worsening heart failure, arrhythmia, or myocardial ischemia during hospitalization.\n\nResultsCardiac events occurred in 146 (6.9%) of 2,107 patients and included episodes of heart failure (n=101, 4.8%), arrhythmia (n=53, 2.5%), and myocardial ischemia (n=14, 0.7%). Cardiac events occurred in 11 of 207 (5.3%), 18 of 250 (7.2%), and 31 of 277 (11.2%) patients exposed to azithromycin, clarithromycin, and erythromycin for at least one day, respectively, and in 9 of 234 (3.8%), 5 of 194 (2.6%), and 23 of 566 (4.1%) patients exposed to ciprofloxacin, levofloxacin, and moxifloxacin, respectively. Hazard ratios for any cardiac event, adjusted for confounding, were 0.89 (95% confidence interval (CI) 0.48 to 1.67), 1.06 (95% CI 0.61 to 1.83) and 1.68 (95% CI 1.07 to 2.62) for azithromycin, clarithromycin, and erythromycin, respectively, and adjusted hazard ratios were 0.86 (95% CI 0.47 to 1.57), 0.42 (95% CI 0.18 to 0.96) and 0.62 (95% CI 0.39 to 0.99) for ciprofloxacin, levofloxacin, and moxifloxacin, respectively. Erythromycin was associated with an adjusted hazard ratio of 2.08 (95% CI 1.25 to 3.46) for heart failure.\n\nLimitationsPossibility of confounding by indication and observational bias\n\nConclusionsAmong patients with CAP hospitalized to non-ICU wards, erythromycin use was associated with a 68% increased risk of hospital-acquired cardiac events, mainly heart failure. Levofloxacin and moxifloxacin were associated with a lower risk of heart failure.\n\nRegistrationThe original trial was registered under ClinicalTrials.gov Identifier NCT01660204\n\nFunding SourceThe Netherlands Organization for Health Research and Development (ZONmw, Health care efficiency research, project id: 171202002).

epidemiology↗

bioRxiv2017

Response Adjusted for Days of Antibiotic Risk (RADAR): evaluation of a novel method to analyze antibiotic stewardship interventions

OBJECTIVESThe Response Adjusted for Days of Antibiotic Risk (RADAR)-statistic was proposed to improve efficiency of antibiotic stewardship trials. We studied the behavior of RADAR in a non-inferiority trial in which a beta-lactam monotherapy strategy (BL, n=656) was non-inferior to fluoroquinolone monotherapy (FQL, n=888) for moderately-severe community-acquired pneumonia (CAP) patients.\n\nMETHODSPatients were ranked according to clinical outcome, using five or eight categories, and antibiotic use. RADAR was calculated as the probability that the BL group had a more favorable ranking than the FQL group. To investigate the sensitivity of RADAR to detrimental clinical outcome we simulated increasing rates of 90-day mortality in the BL group and performed the RADAR and non-inferiority analysis.\n\nRESULTSThe RADAR of the BL-group compared to the FQL group was 60.3% (95% confidence interval 57.9%-62.7%) using five and 58.4% (95% CI 56.0%-60.9%) using eight clinical outcome categories, all in favor of BL. Sample sizes for RADAR were 250 and 580 patients per study arm using five or eight clinical outcome categories, respectively, reflecting 38% and 89% of the original non-inferiority sample size calculation. With simulated mortality rates, loss of non-inferiority of the BL-group occurred at a relative risk of 1.125 in the conventional analysis, whereas using RADAR the BL-group lost superiority at a relative risk of mortality of 1.25 and 1.5, with eight and five clinical outcome categories, respectively.\n\nCONCLUSIONSRADAR favored BL over FQL therapy for CAP. Although RADAR required fewer patients than conventional non-inferiority analysis, the statistic was less sensitive to detrimental outcomes.

epidemiology↗

bioRxiv2017

Gut microbiota and resistome dynamics in intensive care patients receiving selective digestive tract decontamination

BackgroundCritically 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.\n\nResultsDuring 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.\n\nThe 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.\n\nConclusionsThe 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.

microbiology↗

bioRxiv2017

Fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum

Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. Here, we identify genes that contribute to growth of E. faecium in human serum. We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, to completion and then compared its transcriptome during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. A high-throughput transposon sequencing (Tn-seq) approach was used to identify conditionally essential genes in E. faecium E745 during growth in serum. Genes involved in de novo nucleotide biosysnthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants also exhibited significantly attenuated virulence in an intravenous zebrafish infection model. We conclude that genes involved in carbohydrate and nucleotide metabolism of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism.

microbiology↗