The ecological effects of selective decontamination of the digestive tract (SDD) on antimicrobial resistance: a 21-year longitudinal single-centre study

Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study)

OBJECTIVE

Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.

DESIGN

We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.

RESULTS

SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.

CONCLUSION

Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.

Selective decontamination of the digestive tract: concept and application

Selective digestive decontamination (SDD) is a prophylactic strategy aimed at preventing or eradicating bacterial overgrowth in the intestinal flora that precedes the development of most infections in the Intensive Care Unit. SDD prevents serious infections, reduces mortality, is cost-effective, has no adverse effects, and its short- or long-term use is not associated with any significant increase in antimicrobial resistance. SDD is one of the most widely evaluated interventions in critically ill patients, yet its use is not widespread. The present article offers a narrative review of the most relevant evidence and an update of the pathophysiological concepts of infection control supporting the use of SDD.

Ecological effects of selective oral decontamination on multidrug-resistance bacteria acquired in the intensive care unit: a case-control study over 5 years

Purpose

This case–control study investigated the long-term evolution of multidrug-resistant bacteria (MDRB) over a 5-year period associated with the use of selective oropharyngeal decontamination (SOD) in the intensive care unit (ICU). In addition, effects on health care-associated infections and ICU mortality were analysed.

Methods

We investigated patients undergoing mechanical ventilation > 48 h in 11 adult ICUs located at 3 campuses of a university hospital. Administrative, clinical, and microbiological data which were routinely recorded electronically served as the basis. We analysed differences in the rates and incidence densities (ID, cases per 1000 patient-days) of MDRB associated with SOD use in all patients and stratified by patient origin (outpatient or inpatient). After propensity score matching, health-care infections and ICU mortality were compared.

Results

5034 patients were eligible for the study. 1694 patients were not given SOD. There were no differences in the incidence density of MDRB when SOD was used, except for more vancomycin-resistant Enterococcus faecium (0.72/1000 days vs. 0.31/1000 days, p < 0.01), and fewer ESBL-producing Klebsiella pneumoniae (0.22/1000 days vs. 0.56/1000 days, p < 0.01). After propensity score matching, SOD was associated with lower incidence rates of ventilator-associated pneumonia and death in the ICU but not with ICU-acquired bacteremia or urinary tract infection.

Conclusions

Comparisons of the ICU-acquired MDRB over a 5-year period revealed no differences in incidence density, except for lower rate of ESBL-producing Klebsiella pneumoniae and higher rate of vancomycin-resistant Enterococcus faecium with SOD. Incidence rates of ventilator-associated pneumonia and death in the ICU were lower in patients receiving SOD.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00134-022-06826-7.

COVID-19 Secondary Infections in ICU Patients and Prevention Control Measures: A Preliminary Prospective Multicenter Study

The incidence of secondary infections in critically ill coronavirus disease 2019 (COVID-19) patients is worrisome. We investigated whether selective digestive decontamination (SDD) added to infection control measures during an intensive care unit (ICU) stay modified these infection rates. Methods: A retrospective observational cohort study was carried out in four ICUs in Spain. All consecutive ventilated patients with a SARS-CoV-2 infection engaged in national infection control programs between 1 March and 10 December 2020 were investigated. Patients were grouped into two cohorts according to the site of ICU admission. Secondary relevant infections were included. Infection densities corresponding to ventilator-associated pneumonia (VAP), catheter bacteremia, secondary bacteremia, and multi-resistant germs were obtained as the number of events per 1000 days of exposure and were compared between SDD and non-SDD groups using Poisson regression. Factors that had an independent association with mortality were identified using multidimensional logistic analysis. Results: There were 108 patients in the SDD cohort and 157 in the non-SDD cohort. Patients in the SDD cohort showed significantly lower rates (p < 0.001) of VAP (1.9 vs. 9.3 events per 1000 ventilation days) and MDR infections (0.57 vs. 2.28 events per 1000 ICU days) and a non-significant reduction in secondary bacteremia (0.6 vs. 1.41 events per 1000 ICU days) compared with those in the non-SDD cohort. Infections caused by MDR pathogens occurred in 5 patients in the SDD cohort and 21 patients in the non-SDD cohort (p = 0.006). Differences in mortality according to SDD were not found. Conclusion: The implementation of SDD in infection control programs significantly reduced the incidence of VAP and MDR infections in critically ill SARS-CoV-2 infected patients.

A prospective matched case-control study on the genomic epidemiology of colistin-resistant Enterobacterales from Dutch patients

Background

Colistin is a last-resort treatment option for infections with multidrug-resistant Gram-negative bacteria. However, colistin resistance is increasing.

Methods

A six-month prospective matched case-control study was performed in which 22 Dutch laboratories with 32 associated hospitals participated. Laboratories were invited to send a maximum of five colistin-resistant Escherichia coli or Klebsiella pneumoniae (COLR-EK) isolates and five colistin-susceptible isolates (COLS-EK) to the reference laboratory, matched for patient location, material of origin and bacterial species. Epidemiological/clinical data were collected and included in the analysis. Characteristics of COLR-EK/COLS-EK isolates were compared using logistic regression with correction for variables used for matching. Forty-six ColR-EK/ColS-EK pairs were analysed by next-generation sequencing (NGS) for whole-genome multi-locus sequence typing and identification of resistance genes, including mcr genes. To identify chromosomal mutations potentially leading to colistin resistance, NGS reads were mapped against gene sequences of pmrAB, phoPQ, mgrB and crrB.

Results

In total, 72 COLR-EK/COLS-EK pairs (75% E. coli and 25% K. pneumoniae) were included. Twenty-one percent of COLR-EK patients had received colistin, in contrast to 3% of COLS-EK patients (OR > 2.9). Of COLR-EK isolates, five contained mcr-1 and two mcr-9. One isolate lost mcr-9 after repeated sub-culturing, but retained colistin resistance. Among 46 sequenced COLR-EK isolates, genetic diversity was large and 19 (41.3%) isolates had chromosomal mutations potentially associated with colistin resistance.

Conclusions

Colistin resistance is present but uncommon in the Netherlands and caused by the mcr gene in a minority of COLR-EK isolates. There is a need for surveillance of colistin resistance using appropriate susceptibility testing methods.

Enteral Vancomycin to Eliminate MRSA Carriership of the Digestive Tract in Critically Ill Patients

Background: Carriership with methicillin resistant Staphylococcus aureus (MRSA) is a risk for the development of secondary infections in critically ill patients. Previous studies suggest that enteral vancomycin is able to eliminate enteral carriership with MRSA. Data on individual effects of this treatment are lacking. Methods: Retrospective analysis of a database containing 15 year data of consecutive patients from a mixed medical-(cardio)surgical 18 bedded intensive care unit was conducted. All consecutive critically ill patients with enteral MRSA carriership detected in throat and/or rectal samples were collected. We analyzed those with follow-up cultures to determine the success rate of enteral vancomycin. Topical application of 2% vancomycin in a sticky oral paste was performed combined with a vancomycin solution of 500 mg four times daily in the nasogastric tube. This treatment was added to a regimen of selective digestive tract decontamination (SDD) to prevent ICU acquired infection. Results: Thirteen patients were included. The mean age was 65 years and the median APACHE II score was 21. MRSA was present in the throat in 8 patients and in both throat and rectum in 5 patients. In all patients MRSA was successfully eliminated from both throat and rectum, which took 2–11 days with a median duration until decontamination of 4 days. Secondary infections with MRSA did not occur. Conclusions: Topical treatment with vancomycin in a 2% sticky oral paste four times daily in the nasogastric tube was effective in all patients in the elimination of MRSA and prevented secondary MRSA infections.

Eradication of Resistant and Susceptible Aerobic Gram-Negative Bacteria From the Digestive Tract in Critically Ill Patients; an Observational Cohort Study

BACKGROUND

Selective Decontamination of the Digestive tract (SDD) aims to prevent nosocomial infections, by eradication of potentially pathogenic micro-organisms from the digestive tract.

OBJECTIVES

To estimate the rate of and the time to eradication of resistant vs. susceptible facultative aerobic gram-negative bacteria (AGNB) in patients treated with SDD.

METHODS

This observational and retrospective study included patients admitted to the ICU between January 2001 and August 2017. Patients were included when treated with SDD (tobramycin, polymyxin B, and amphotericin B) and colonized in the upper or lower gastro-intestinal (GI) tract with at least one AGNB present on admission. Decontamination was determined after the first negative set of cultures (rectal and throat). An additional analysis was performed of two consecutive negative cultures.

RESULTS

Of the 281 susceptible AGNB in the throat and 1,087 in the rectum on admission, 97.9 and 93.7%, respectively, of these microorganisms were successfully eradicated. In the upper GI-tract no differences in eradication rates were found between susceptible and resistant microorganisms. However, the median duration until eradication was significantly longer for aminoglycosides resistant vs. susceptible microorganisms (5 vs. 4 days, p < 0.01). In the lower GI-tract, differences in eradication rates between susceptible and resistant microorganisms were found for cephalosporins (90.0 vs. 95.6%), aminoglycosides (84.4 vs. 95.5%) and ciprofloxacin (90.0 vs. 95.2%). Differences in median duration until eradication between susceptible and resistant microorganisms were found for aminoglycosides and ciprofloxacin (both 5 days vs. 6 days, p = 0.001). Decontamination defined as two negative cultures was achieved in a lower rate (77-98% for the upper GI tract and 64-77% for the lower GI tract) and a median of 1 day later.

CONCLUSION

The vast majority of both susceptible and resistant microorganisms are effectively eradicated from the upper and lower GI tract. In the lower GI tract decontamination rates of susceptible microorganisms are significantly higher and achieved in a shorter time period compared to resistant strains.

Selective Intestinal Decontamination as a Method for Preventing Infectious Complications (Review)

Infectious complications are the most common cause of death in patients with severe burns. To date, there is no generally accepted method for preventing such complications in burn injury. One of the possible prevention options is selective intestinal decontamination (SID). This method is based on the enteral administration of non-absorbable antimicrobial agents. The preventive effect of SID involves inhibition of intestinal microflora translocation through the mucous membranes, inasmuch as studies demonstrate that endogenous opportunistic microorganisms are a common cause of infectious complications in various critical conditions.

The SID method was originally developed in the Netherlands for patients suffering from mechanical injury. Antimicrobial drugs were selected based on their high activity in relation to the main endogenous opportunistic pathogens and minimal activity against normal intestinal microflora components. The combination of polymyxin (B or E), tobramycin, and amphotericin B with intravenous cefotaxime was chosen as the first SID regimen. Other regimens were proposed afterwards, and the application field of the method was expanded. In particular, it became the method of choice for prevention of infectious complications in patients with severe burn injury.

Clinical studies demonstrate efficacy of some SID regimens for preventing infectious complications in patients with thermal injury. Concomitant administration of SID and systemic preventive antibiotics and addition of oropharyngeal decontamination increases the method efficacy. SID is generally well-tolerated, but some studies show an increased risk of diarrhea with this preventive option. In addition, SID increases the risk of developing antibiotic resistance like any other antibiotic regimens.

Gut microbiota and sepsis: from pathogenesis to novel treatments

PURPOSE OF REVIEW

This review summarizes recent progress in our understanding of the role of the gut microbiota in sepsis pathogenesis and outlines the potential role of microbiota-targeted therapies.

RECENT FINDINGS

The composition of the gut microbiome is profoundly distorted during sepsis, with a loss of commensal bacteria and an overgrowth of potential pathogenic micro-organisms. These alterations also extend to nonbacterial intestinal inhabitants. Disruptions of these intestinal communities are associated with both an increased susceptibility to develop sepsis, as well as a higher risk of adverse outcomes. Preclinical studies have characterized the effects of several microbiota-derived metabolites (such as D-lactate, butyrate, and deoxycholic acid) on enhancing the host immune response during critical illness. Microbiota-targeted therapies (e.g. probiotics or fecal microbiota transplantation) might be of benefit, but can also be associated with increased risks of bloodstream infections.

SUMMARY

Emerging evidence display an important role of gut micro-organisms (including bacteria, fungi, eukaryotic viruses, and bacteriophages) and their derived metabolites in both the susceptibility to, as well as outcomes of sepsis. Despite recent progress in the mechanistic understanding of microbiota-mediated protection, clinical breakthroughs in the development of microbiota-based prognostic tools or therapies are thus far lacking in the field of sepsis.

Anti-infectious decontamination strategies in Dutch intensive care units: A survey study on contemporary practice and heterogeneity

PURPOSE

Despite increasing evidence and updated national guidelines, practice of anti-infectious strategies appears to vary in the Netherlands. This study aimed to determine the variation of current practices of anti-infectious strategies in Dutch ICUs.

MATERIALS AND METHODS

In 2018 and 2019 an online survey of all Dutch ICUs was conducted with detailed questions on their anti-infectious strategies.

RESULTS

89% (63 of 71) of the Dutch ICUs responded to the online survey. The remaining ICUs were contacted by telephone. 47 (66%) of the Dutch ICUs used SDD, 14 (20%) used SOD and 10 (14%) used neither SDD nor SOD. Within these strategies considerable heterogeneity was observed in the start criteria of SDD/SOD, the regimen adjustments based on microbiological surveillance and the monitoring of the interventions.

CONCLUSIONS

The proportion of Dutch ICUs applying SDD or SOD increased over time. Considerable heterogeneity in the regimens was reported. The impact of the observed differences within SDD and SOD practices on clinical outcome remains to be explored.

Reducing the dosing frequency of selective digestive tract decontamination to three times daily provides effective decontamination of Gram-negative bacteria

This study evaluated the effectiveness of selective digestive tract decontamination (SDD) application three times daily (t.i.d.) compared to the standard four times daily (q.i.d.). Retrospective equivalence (combined non-inferiority and non-superiority design) study with a before-and-after design on a tertiary ICU in which the SDD frequency was reduced from q.i.d. to t.i.d. All patients with ICU admissions ≥72h and with ≥2 surveillance cultures collected on different dates were included in this study. We compared successful decontamination of Gram-negative bacteria (GNB). Furthermore, time to decontamination, ICU-acquired GNB bacteraemia and 28-day mortality were compared between the two groups. In total 1958 ICU admissions (1236 q.i.d., 722 t.i.d). Decontamination was achieved during the first week of admission in 77% and 76% of patients receiving SDD q.i.d and t.i.d., respectively. Successful decontamination within 14 days (without consecutive acquisition of Gram-negative bacteria) was achieved in 69.3% of the admissions with q.i.d. versus 66.8% in t.i.d. SDD (p-value = 0.2519). The proportions of successful decontamination of GNB were equivalent in both groups (−0.025, 98% CI: −0.087; 0.037). There was no significant difference in time to decontamination between the two regimens (log-rank test p-value = 0.55). Incidence (episodes/1000 days) of ICU-acquired GNB bacteraemia was 0.9 in both groups, and OR for death at day 28 in the t.i.d. group compared to the q.i.d. group was 0.99 (95% confidence interval, 0.80–1.21). This study shows that a t.i.d. application regimen achieves similar outcomes to the standard q.i.d. regime, for both microbiological and clinical outcome measures.

Impact of microbiome-based interventions on gastrointestinal pathogen colonization in the intensive care unit

In the intensive care unit (ICU), colonization of the gastrointestinal tract by potentially pathogenic bacteria is common and often precedes clinical infection. Though effective in the short term, traditional antibiotic-based decolonization methods may contribute to rising resistance in the long term. Novel therapies instead focus on restoring gut microbiome equilibrium to achieve pathogen colonization resistance. This review summarizes the existing data regarding microbiome-based approaches to gastrointestinal pathogen colonization in ICU patients with a focus on prebiotics, probiotics, and synbiotics.

Decreased duration of intravenous cephalosporins in intensive care unit patients with selective digestive decontamination: a retrospective before-and-after study

Selective digestive decontamination (SDD) reduces the rate of infection and improves the outcomes of patients admitted to an intensive care unit (ICU). A risk associated with its use is the development of multi-drug-resistant organisms. We hypothesized that a 1-day reduction in systemic antimicrobial exposure in the SDD regimen would not affect the outcomes of our patients. In this before-and-after study design, 199 patients and 248 patients were included in a 3-day SDD group and a 2-day SDD group, respectively. The rates of hospital-acquired pneumonia and ICU infections were similar in both groups. The rates of bloodstream infection and bacteriuria were significantly lower in the 2-day SDD group than in the 3-day SDD group. Compared with the patients in the 3-day group, the patients in the 2-day SDD group received fewer antibiotics and less exposure to mechanical ventilation, and they used fewer ICU resources. The rates of ICU mortality and 28-day mortality were similar in both groups. The incidence of multi-drug-resistant organisms was similar in both groups. Within the limitations inherent to our study design, reducing the exposure of prophylactic systemic antibiotics in the SDD setting from 3 days to 2 days was not associated with impaired outcomes. Future randomized controlled trials should be conducted to test this hypothesis and investigate the effects on the development of multi-drug resistant organisms.

Attenuation of MODS-related and ARDS-related mortality makes infectious complications a remaining challenge in the severely injured

Introduction

The recent decrease in multiple organ dysfunction syndrome (MODS)-associated and adult respiratory distress syndrome (ARDS)-associated mortality could be considered a success of improvements in trauma care. However, the incidence of infections remains high in patients with polytrauma, with high morbidity and hospital resources usage. Infectious complications might be a residual effect of the decrease in MODS-related/ARDS-related mortality. This study investigated the current incidence of infectious complications in polytrauma.

Methods

A 5.5-year prospective population-based cohort study included consecutive severely injured patients (age >15) admitted to a (Level-1) trauma center intensive care unit (ICU) who survived >48 hours. Demographics, physiologic and resuscitation parameters, multiple organ failure and ARDS scores, and infectious complications (pneumonia, fracture-related infection, meningitis, infections related to blood, wound, and urinary tract) were prospectively collected. Data are presented as median (IQR), p<0.05 was considered significant.

Results

297 patients (216 (73%) men) were included with median age of 46 (27–60) years, median Injury Severity Score was 29 (22–35), 96% sustained blunt injuries. 44 patients (15%) died. One patient (2%) died of MODS and 1 died of ARDS. 134 patients (45%) developed 201 infectious complications. Pneumonia was the most common complication (50%). There was no difference in physiologic parameters on arrival in emergency department and ICU between patients with and without infectious complications. Patients who later developed infections underwent more often a laparotomy (32% vs 18%, p=0.009), had more often pelvic fractures (38% vs 25%, p=0.02), and received more blood products <8 hours. They had more often MODS (25% vs 13%, p=0.005), stayed longer on the ventilator (10 (5–15) vs 5 (2–8) days, p<0.001), longer in ICU (11 (6–17) vs 6 (3–10) days, p<0.001), and in hospital (30 (20–44) vs 16 (10–24) days, p<0.001). There was however no difference in mortality (12% vs 17%, p=0.41) between both groups.

Conclusion

45% of patients developed infectious complications. These patients had similar mortality rates, but used more hospital resources. With low MODS-related and ARDS-related mortality, infections might be a residual effect, and are one of the remaining challenges in the treatment of patients with polytrauma.

Level of evidence

Level 3.

Study type

Population-based cohort study.

Selective decontamination of the digestive tract (SDD) in critically ill patients: a narrative review

Selective decontamination of the digestive tract (SDD) is an infection prevention measure for intensive care unit (ICU) patients that was proposed more than 30 years ago, and that is currently considered standard of care in the Netherlands, but only used sporadically in ICUs in other countries. In this narrative review, we first describe the rationale of the individual components of SDD and then review the evidence base for patient-centered outcomes, where we distinguish ICUs with low prevalence of antibiotic resistance from ICUs with moderate–high prevalence of resistance. In settings with low prevalence of antibiotic resistance, SDD has been associated with improved patient outcome in three cluster-randomized studies. These benefits were not confirmed in a large international cluster-randomized study in settings with moderate-to-high prevalence of antibiotic resistance. There is no evidence that SDD increases antibiotic resistance. We end with future directions for research.