Impact of antimicrobial therapy on the gut microbiome

Modeling the Effect of DAV132, a Novel Colon-Targeted Adsorbent, on Fecal Concentrations of Moxifloxacin and Gut Microbiota Diversity in Healthy Volunteers

To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract, was developed. We built an integrated pharmacological model of how DAV132 reduces fecal free moxifloxacin and preserves gut microbiota. We used plasma and fecal free moxifloxacin concentrations, and Shannon diversity index from 16S ribosomal RNA gene metagenomics analysis of fecal microbiota, of 143 healthy volunteers assigned randomly to receive moxifloxacin only, or with 10 DAV132 dose regimens, or to a control group. We modeled reduced fecal moxifloxacin concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of the amount of activated charcoal on adsorption efficacy. Changes in moxifloxacin-induced perturbations on gut microbiota diversity were then quantified through a turnover model with the Emax model. With the developed model, the efficiency of pharmacokinetic antagonism and its consequences on gut microbiota diversity were quantified.

An overview of guidelines for the management of hospital-acquired and ventilator-associated pneumonia caused by multidrug-resistant Gram-negative bacteria

PURPOSE OF REVIEW

Multidrug-resistant (MDR) Gram-negative pathogens in hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) are associated with poor clinical outcomes. These pathogens represent a global threat with few therapeutic options. In this review, we discuss current guidelines for the empiric management of HAP/VAP caused by MDR Gram-negative pathogens.

RECENT FINDINGS

The incidence of MDR Gram-negative bacteria is rising among cases of nosocomial pneumonia, such that it is now becoming a significant challenge for clinicians. Adherence to international guidelines may ensure early and adequate antimicrobial therapy, guided by local microbiological data and awareness of the risk factors for MDR bacteria.

SUMMARY

Due to the increasing prevalence of HAP/VAP caused by MDR Gram-negative pathogens, management should be guided by the local ecology and the patient's risk factors for MDR pathogens. The main risk factors are prior hospitalization for at least 5 days, prior use of broad-spectrum antibiotics, prior colonization with resistant pathogens, admission to hospital settings with high rates of MDR pathogens, and septic shock at the time of diagnosis with nosocomial pneumonia.

Low-dose antibiotic prophylaxis has no significant impact on the stability of the intestinal microbiome in children with urogenital tract malformations under 1 year of age

INTRODUCTION

Accumulating data point at potentially lasting effects of early childhood therapeutic antibiotic exposure on the intestinal microbial. Little is known on the impact of low-dose longterm antibiotic prophylaxis on the developing intestinal microbiota in children during their first year of life.

OBJECTIVE

To investigate compositional changes of the intestinal microbiota by next generation sequencing based microbiome analysis and bacterial metabolites in longitudinally collected fecal samples.

STUDY DESIGN

Twelve patients were analyzed in this prospective, longitudinal pilot study during a period of 70 days (sampling on days 0,7,14,30,70). Only transvaginally and term born babies, breastfed with no prior antibiotic exposure with urogenital malformation (vesicoureteral reflux and/or upper urinary tract dilatation) were included into the study. Seven patients received antibiotic longterm prophylaxis with a second-generation cephalosporin and five did not. Sequencing of bacterial 16 S rRNA allowed for an analysis of the microbiome composition. The Principal coordinate analysis was performed for the evaluation of compositional profile. Furthermore, quantitative measurement of short chain fatty acids served as a proxy for the metabolic activity of the individual microbiome over the study time.

RESULTS

Analysis of observed species, Shannon Index and weighted Unifrac distances between timepoints revealed neither significant difference comparing the prophylaxis group versus the control group over the study period, nor significant changes within the groups over time. Principal coordinate analysis (PCoA) was performed for the evaluation of compositional profile. Also, no differences regarding the fecal SCFA content were found between the two groups (>0.05 at each tested point, Mann-Whitney Test).

DISCUSSION

Although there were interindividual compositional differences of the microbiome (cluster of bacterial composition) at the beginning of the observation, we did not observe significant longitudinal changes regarding both bacterial diversity and SCFAs in neither group. Over the study period, the patient's microbiome remained stable and resilient to the antibiotic exposure in terms of bacterial abundance and metabolism. Limitations to the study are the low number of patients included and the use of one single antibiotic (cefaclor).

CONCLUSION

This is the first pilot study to demonstrate that long term low-dose antibiotic administration in children under one year of age does neither seem to influence the composition of the intestinal microbiota nor the quantities of bacterial fermentation products compared to untreated controls.

Antibiotics impair immune checkpoint inhibitor effectiveness in Hispanic patients with non-small cell lung cancer (AB-CLICaP)

Background

The intestinal microbiota is an important factor in modulating immune‐mediated tumor cell destruction. Alterations in the microbiome composition have been linked to reduced efficacy of immune checkpoint inhibitor (ICI) therapies. Therefore, antibiotic treatment (ATB), which modifies the diversity of the gut bacteria populations, could lead to a reduced efficacy of ICI treatments.

Methods

This was a retrospective cohort study. Patients with advanced non‐small cell lung cancer (NSCLC) treated with anti‐programmed cell death ligand‐1 (PD‐L1) alone, or in combination in three different countries in Latin America were included. After identification, patients were placed into three groups: Non‐ATB exposed (no‐ATB), exposed within 30 days of the first dose of ICI (pre‐ICI ATB) and patients receiving ATB concomitantly with ICI (ICI‐ATB). Progression‐free survival (PFS), overall survival (OS) and response rates to treatment with ICI were assessed.

Results

A total of 140 patients were included, of which 32 patients (23%) received ATB treatment. The most common ATB types were fluoroquinolones and B‐lactams. No differences in survival according to antibiotic type were identified. Median OS in patients not exposed to ATB was 40.6 months (95% CI: 32–67.7), compared with 20.3 months (95% CI: 12.1‐non‐reached [NR]) for patients with pre‐ICI ATB treatment and 24.7 months (95% CI: 13‐NR) for patients treated with ATB concomitantly with ICI. There were no significant differences in terms of PFS, or response rates across all treatment groups.

Conclusions

Antibiotic treatment was associated with reduced OS in Hispanic patients with NSCLC treated with ICIs.

Sniffing Out Urinary Tract Infection-Diagnosis Based on Volatile Organic Compounds and Smell Profile

Current available methods for the clinical diagnosis of urinary tract infection (UTI) rely on a urine dipstick test or culturing of pathogens. The dipstick test is rapid (available in 1-2 min), but has a low positive predictive value, while culturing is time-consuming and delays diagnosis (24-72 h between sample collection and pathogen identification). Due to this delay, broad-spectrum antibiotics are often prescribed immediately. The over-prescription of antibiotics should be limited, in order to prevent the development of antimicrobial resistance. As a result, there is a growing need for alternative diagnostic tools. This paper reviews applications of chemical-analysis instruments, such as gas chromatography-mass spectrometry (GC-MS), selected ion flow tube mass spectrometry (SIFT-MS), ion mobility spectrometry (IMS), field asymmetric ion mobility spectrometry (FAIMS) and electronic noses (eNoses) used for the diagnosis of UTI. These methods analyse volatile organic compounds (VOCs) that emanate from the headspace of collected urine samples to identify the bacterial pathogen and even determine the causative agent's resistance to different antibiotics. There is great potential for these technologies to gain wide-spread and routine use in clinical settings, since the analysis can be automated, and test results can be available within minutes after sample collection. This could significantly reduce the necessity to prescribe broad-spectrum antibiotics and allow the faster and more effective use of narrow-spectrum antibiotics.

Identification and characterization of novel small molecule inhibitors to control Mycoplasma gallisepticum infection in chickens

Mycoplasma gallisepticum (MG) causes chronic respiratory disease in chickens, leading to severe economic losses to the poultry industry. Currently the disease is managed with antimicrobials and vaccination; however, emergence of multi-drug resistant Mycoplasma and the limited effect of vaccines necessitate development of novel approaches. A library of 4,182 small molecules (SMs) was screened for identification of narrow spectrum anti-MG compounds using high throughput screening. A total of 584 SMs were identified. Ten SMs possessed low MICs (0.78-100 μM) with efficacy against multiple MG strains and MG biofilm. These 10 SMs did not affect commensal/probiotic bacteria and other avian and foodborne pathogens. They displayed no or little toxicity on the avian macrophage HD-11 cells, human epithelial Caco-2 cells, and chicken red blood cells (RBCs); but, they were effective in reducing MG in chicken RBCs. Six SMs (SM1, SM3-5, and SM9-10) were tested in three-week-old chickens infected with MG (nasal spray; 10⁹ CFU/bird). SM4 and SM9 reduced airsacculitis by 77.2 % and 82.9 %, MG load in the trachea by 0.9 log (p < 0.05) and 2.7 log (p < 0.0001), and tracheal mucosal thickness by 23 % and 61 %, respectively with no impact on the richness and evenness of the cecal (P = 0.6; H = 1.0) and tracheal (P = 0.8; H = 0.8) microbiota compared to the MG-infected controls. Both SM4 and SM9 treatments resulted in a significant alteration in the cell membrane conformation of MG. In conclusion; we identified two novel growth inhibitors of MG that are effective in chickens. These findings will facilitate development of novel antibacterials to control mycoplasmosis in poultry.

Postbiotic-Enabled Targeting of the Host-Microbiota-Pathogen Interface: Hints of Antibiotic Decline?

Mismanagement of bacterial infection therapies has undermined the reliability and efficacy of antibiotic treatments, producing a profound crisis of the antibiotic drug market. It is by now clear that tackling deadly infections demands novel strategies not only based on the mere toxicity of anti-infective compounds. Host-directed therapies have been the first example as novel treatments with alternate success. Nevertheless, recent advances in the human microbiome research have provided evidence that compounds produced by the microbial metabolism, namely postbiotics, can have significant impact on human health. Such compounds target the host-microbe-pathogen interface rescuing biotic and immune unbalances as well as inflammation, thus providing novel therapeutic opportunities. This work discusses critically, through literature review and personal contributions, these novel nonantibiotic treatment strategies for infectious disease management and resistance prevention, which could represent a paradigm change rocking the foundation of current antibiotic therapy tenets.

Altered Patterns of Compositional and Functional Disruption of the Gut Microbiota in Typhoid Fever and Nontyphoidal Febrile Illness

BACKGROUND

Experimental murine models and human challenge studies of Salmonella Typhi infection have suggested that the gut microbiome plays an important protective role against the development of typhoid fever. Anaerobic bacterial communities have been hypothesized to mediate colonization resistance against Salmonella species by producing short-chain fatty acids, yet the composition and function of the intestinal microbiota in human patients with typhoid fever remain ill defined.

METHODS

We prospectively collected fecal samples from 60 febrile patients admitted to Chittagong Medical College Hospital, Bangladesh, with typhoid fever or nontyphoidal febrile illness and from 36 healthy age-matched controls. The collected fecal samples were subjected to 16s rRNA sequencing followed by targeted metabolomics analysis.

RESULTS

Patients with typhoid fever displayed compositional and functional disruption of the gut microbiota compared with patients with nontyphoidal febrile illness and healthy controls. Specifically, typhoid fever patients had lower microbiota richness and alpha diversity and a higher prevalence of potentially pathogenic bacterial taxa. In addition, a lower abundance of short-chain fatty acid-producing taxa was seen in typhoid fever patients. The differences between typhoid fever and nontyphoidal febrile illness could not be explained by a loss of colonization resistance after antibiotic treatment, as antibiotic exposure in both groups was similar.

CONCLUSIONS

his first report on the composition and function of the gut microbiota in patients with typhoid fever suggests that the restoration of these intestinal commensal microorganisms could be targeted using adjunctive, preventive, or therapeutic strategies.

Antimicrobial De-Escalation in the ICU: From Recommendations to Level of Evidence

Antimicrobial de-escalation (ADE) is a component of antimicrobial stewardship (AMS) aimed to reduce exposure to broad-spectrum antimicrobials. In the intensive care unit, ADE is a strong recommendation that is moderately applied in clinical practice. Following a systematic review of the literature, we assessed the studies identified on the topic which included one randomized controlled trial and 20 observational studies. The literature shows a low level of evidence, although observational studies suggested that this procedure is safe. The effects of ADE on the level of resistance of ecological systems and especially on the microbiota are unclear. The reviewers recommend de-escalating antimicrobial treatment in patients requiring long-term antibiotic therapy and considering de-escalation in short-term treatments.

Effective implementation of the Accelerate Pheno™ system for positive blood cultures

Using conventional methods, organism identification (ID) and antibiotic susceptibility testing (AST) results are available ∼1.5–3 days after positive blood culture. New technologies can reduce this time to 8–12 h, allowing therapy to be optimized substantially sooner. To make full use of fast ID and AST results requires overcoming various hurdles to effective implementation, including restructuring laboratory workflows to optimize timeliness of results and modifying clinical pathways to respond more quickly when results are available. Efficient laboratory procedures and clinical interventions coupled with fast and accurate identification and AST results have the potential to substantially reduce overall costs and provide more-sophisticated and effective patient management.

Combined influence of practice guidelines and prospective audit and feedback stewardship on antimicrobial treatment of community-acquired pneumonia and empyema in children: 2012 to 2016

Background

Aminopenicillins are recommended empiric therapy for community-acquired pneumonia (CAP). The aim of the study was to assess treatment over a 5-year period after CAP guideline publication and introduction of an antimicrobial stewardship program (ASP).

Methods

Using ICD-10 discharge codes for pneumonia, children less than 18 years admitted to the Children's Hospital of Eastern Ontario January 1, 2012 and December 31, 2016 were identified. Children ≥ 2 months with consolidation were included. One day of therapy (DOT) was one or more doses of an antimicrobial given for 1 day.

Results

Of 1,707 patients identified, 713 met inclusion criteria. Eighteen (2.5%) had bacteria identified by culture and 79 of 265 (29.8%) had Mycoplasma pneumoniae detected. Mean DOT/1,000 patient days of aminopenicillins/penicillin (AAP) increased by 18.1% per year (95% confidence interval [CI] -0.2, 39.9%) and decreased by 37.6% per year (95% CI -56.1, -11.3%) for second- and third-generation cephalosporins in the post-ASP period. The duration of discharge antimicrobials decreased. Of 74 (10.4%) patients who had pleural fluid drained, 35 (47.3%) received more than 5 days of AAP and ≤ 5 days of second-/third-generation cephalosporins with no difference in median length of stay nor mean duration of antimicrobials.

Conclusions

Implementation of CAP management guidelines followed by prospective audit and feedback stewardship was associated with a sustained decrease in the use of broad-spectrum antibiotics in childhood CAP. Use of AAP should also be strongly considered in patients with effusions (even if no pathogen is identified), as clinical outcome appears similar to patients treated with broad-spectrum antimicrobials.

Persistence of wastewater antibiotic resistant bacteria and their genes in human fecal material

Domestic wastewater is a recognized source of antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs), whose risk of transmission to humans cannot be ignored. The fitness of wastewater ARB in the complex fecal microbiota of a healthy human was investigated in feces-based microcosm assays (FMAs). FMAs were inoculated with two wastewater isolates, Escherichia coli strain A2FCC14 (MLST ST131) and Enterococcus faecium strain H1EV10 (MLST ST78), harboring the ARGs blaTEM, blaCTX, blaOXA-A and vanA, respectively. The FMAs, incubated in the presence or absence of oxygen or in the presence or absence of the antibiotics cefotaxime or vancomycin, were monitored based on cultivation, ARGs quantification and bacterial community analysis. The fecal bacterial community was dominated by members of the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The ARGs harbored by the wastewater isolates could be quantified after one week, in FMAs incubated under both aerobic and anaerobic conditions. These observations were not significantly different in FMAs incubated anaerobically, supplemented with sub-inhibitory concentrations of cefotaxime or vancomycin. The observation that ARGs of wastewater ARB persisted in presence of the human fecal microbiota for at least one week supports the hypothesis of a potential transmission to humans, a topic that deserves further investigation.

Antibiotic stewardship in the PICU: Impact of ward rounds led by paediatric infectious diseases specialists on antibiotic consumption

Antimicrobial stewardship programmes (ASP) are aimed at optimising antimicrobial utilization. However, only few studies have focused on paediatric intensive care units (PICU), where inappropriate antibiotic use occurs frequently. We assessed the effect and safety of a once weekly paediatric infectious disease (PID) ward round with prospective audit and feedback on antibiotic consumption in a multidisciplinary PICU. This study was conducted within 6-months periods before and after the implementation of a weekly PID-ward round. Antimicrobial management and two main recommendations per patient were discussed and documented. The primary outcome was antimicrobial utilization, measured by days of therapy (DoT) and length of therapy (LoT) per 1000 patient days (PD) for all PICU stays. Secondary outcomes included PICU mean length of stay, total mortality, infection-related mortality and cost of therapy. 1964 PD were analyzed during the pre- and 1866 PD during the post-implementation phase. Adherence to the recommendations was 79%. An 18% reduction of DoT/1000 PD was observed in the post-implementation period (p = 0.005). LoT/1000 PD decreased by 11% (p = 0.09). Meropenem and vancomycin usage were reduced by 49% (p = 0.07) and 56% (p = 0.03), respectively. We conclude, that a once weekly PID-ward round with prospective audit and feedback is safe and effective and reduces antibiotic consumption in PICUs.

Proprietary non-animal stabilized hyaluronic acid/dextranomer gel (NASHA/Dx) for endoscopic treatment of grade IV vesicoureteral reflux: Long-term observational study

BACKGROUND

Since 1993, children aged >1 year with persistent grade III-V vesicoureteral reflux (VUR) and febrile urinary tract infections (UTIs) attending Uppsala University Hospital have undergone endoscopic injection with proprietary non-animal stabilized hyaluronic acid/dextranomer gel (NASHA/Dx; Deflux®).

OBJECTIVE

Investigate long-term incidence of UTI, bladder dysfunction, ureteral reimplantation and overall clinical findings following endoscopic injection of NASHA/Dx.

STUDY DESIGN

Children with grade IV VUR diagnosed by voiding cystourethrogram (VCUG) and dilating VUR persisting for >1 year were included in this study. 15-25 years after endoscopic treatment, patients' hospital charts were studied. Information on bladder function and UTIs was obtained via questionnaire, 8-18 years after endoscopic treatment.

RESULTS

185 patients (69 boys, 116 girls) were included in the study; 237 grade IV VUR ureters were treated. All study patients were diagnosed with VUR after a febrile UTI (i.e. pyelonephritis). According to the last voiding cystourethrogram, 69% of ureters showed a positive response (VUR grade 0-I), 7% had VUR grade II and 23% had VUR grade ≥ III. 46 patients (25%) required ureteral reimplantation during follow-up. Among patients treated during the second 5-year period compared with the first (1998-2003 versus 1993-1998), there was a significant decrease in the rate of ureteral reimplantation (31% vs 16%; p = 0.0365). This difference may be attributable to developments over time in the injection technique. UTIs occurred in 30 patients (21% of the evaluable population): 28 females and 2 males. Febrile UTIs were reported in 14 patients (10%), all females. Forty-nine patients (34%) had bladder problems (e.g. underactivity, overactivity, incontinence). Five patients underwent ureteral reimplantation 'late', 6-10 years after the last endoscopic injection. In one male patient, calcification around the NASHA/Dx implantation site was observed during routine examination 2 years after endoscopic treatment; no intervention was required. No safety issues were observed in the remaining 97% of the study population.

CONCLUSIONS

This study represents the longest published follow-up of Grade IV VUR patients undergoing endoscopic treatment. Three-quarters of patients did not need ureteral reimplantation. Optimal injection technique and higher injection volume were associated with a reduced ureteral reimplantation rate. Treatment with NASHA/Dx was durable and well tolerated: long-term risks of UTI, bladder dysfunction and recurrent VUR were low.

Prevalence of Antibiotic-Resistant Pathogens in Culture-Proven Sepsis and Outcomes Associated With Inadequate and Broad-Spectrum Empiric Antibiotic Use

IMPORTANCE

Broad-spectrum antibiotics are recommended for all patients with suspected sepsis to minimize the risk of undertreatment. However, little is known regarding the net prevalence of antibiotic-resistant pathogens across all patients with community-onset sepsis or the outcomes associated with unnecessarily broad empiric treatment.

OBJECTIVE

To elucidate the epidemiology of antibiotic-resistant pathogens and the outcomes associated with both undertreatment and overtreatment in patients with culture-positive community-onset sepsis.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study included 17 430 adults admitted to 104 US hospitals between January 2009 and December 2015 with sepsis and positive clinical cultures within 2 days of admission. Data analysis took place from January 2018 to December 2019.

EXPOSURES

Inadequate empiric antibiotic therapy (ie, ≥1 pathogen nonsusceptible to all antibiotics administered on the first or second day of treatment) and unnecessarily broad empiric therapy (ie, active against methicillin-resistant Staphylococcus aureus [MRSA]; vancomycin-resistant Enterococcus [VRE]; ceftriaxone-resistant gram-negative [CTX-RO] organisms, including Pseudomonas aeruginosa; or extended-spectrum β-lactamase [ESBL] gram-negative organisms when none of these were isolated).

MAIN OUTCOMES AND MEASURES

Prevalence and empiric treatment rates for antibiotic-resistant organisms and associations of inadequate and unnecessarily broad empiric therapy with in-hospital mortality were assessed, adjusting for baseline characteristics and severity of illness.

RESULTS

Of 17 430 patients with culture-positive community-onset sepsis (median [interquartile range] age, 69 [57-81] years; 9737 [55.9%] women), 2865 (16.4%) died in the hospital. The most common culture-positive sites were urine (9077 [52.1%]), blood (6968 [40.0%]), and the respiratory tract (2912 [16.7%]). The most common pathogens were Escherichia coli (5873 [33.7%]), S aureus (3706 [21.3%]), and Streptococcus species (2361 [13.5%]). Among 15 183 cases in which all antibiotic-pathogen susceptibility combinations could be calculated, most (12 398 [81.6%]) received adequate empiric antibiotics. Empiric therapy targeted resistant organisms in 11 683 of 17 430 cases (67.0%; primarily vancomycin and anti-Pseudomonal β-lactams), but resistant organisms were uncommon (MRSA, 2045 [11.7%]; CTX-RO, 2278 [13.1%]; VRE, 360 [2.1%]; ESBLs, 133 [0.8%]). The net prevalence for at least 1 resistant gram-positive organism (ie, MRSA or VRE) was 13.6% (2376 patients), and for at least 1 resistant gram-negative organism (ie, CTX-RO, ESBL, or CRE), it was 13.2% (2297 patients). Both inadequate and unnecessarily broad empiric antibiotics were associated with higher mortality after detailed risk adjustment (inadequate empiric antibiotics: odds ratio, 1.19; 95% CI, 1.03-1.37; P = .02; unnecessarily broad empiric antibiotics: odds ratio, 1.22; 95% CI, 1.06-1.40; P = .007).

CONCLUSIONS AND RELEVANCE

In this study, most patients with community-onset sepsis did not have resistant pathogens, yet broad-spectrum antibiotics were frequently administered. Both inadequate and unnecessarily broad empiric antibiotics were associated with higher mortality. These findings underscore the need for better tests to rapidly identify patients with resistant pathogens and for more judicious use of broad-spectrum antibiotics for empiric sepsis treatment.

Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts

Long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, and patients with advanced dementia are particularly vulnerable to multidrug-resistant organism (MDRO) acquisition and antimicrobial overuse. In this study, we longitudinally examined a group of patients with advanced dementia using metagenomic sequencing. We found significant inter- and intra-subject heterogeneity in microbiota composition, suggesting temporal instability. We also observed a link between the antimicrobial resistance gene density in a sample and the relative abundances of several pathobionts, particularly Escherichia coli, Proteus mirabilis, and Enterococcus faecalis, and used this relationship to predict resistance gene density in samples from additional subjects. Furthermore, we used metagenomic assembly to demonstrate that these pathobionts had higher resistance gene content than many gut commensals. Given the frequency and abundances at which these pathobionts were found in this population and the underlying vulnerability to MDRO of patients with advanced dementia, attention to microbial blooms of these species may be warranted.

Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms

A clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Although broad-spectrum antibiotics have been shown to disrupt the structure of the gut microbiota, some antibiotics appear to increase CDAD risk without being highly active against intestinal anaerobes, suggesting direct nonantimicrobial effects. We examined cell biological effects of antibiotic exposure that may be involved in bacterial pathogenesis using an in vitro germfree human colon epithelial culture model. We found a marked loss of mucosal barrier and immune function with exposure to the CDAD-associated antibiotics clindamycin and ciprofloxacin, distinct from the results of pretreatment with an antibiotic unassociated with CDAD, tigecycline, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent gut mucosal barrier changes in the increased risk of CDAD with specific antibiotics and warrant further studies in in vivo systems. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD.

Gut microbiota in surgical and critically ill patients

Microbiota-defined as a collection of microbial organisms colonising different parts of the human body-is now recognised as a pivotal element of human health, and explains a large part of the variance in the phenotypic expression of many diseases. A reduction in microbiota diversity, and replacement of normal microbes with non-commensal, pathogenic or more virulent microbes in the gastrointestinal tract-also known as gut dysbiosis-is now considered to play a causal role in the pathogenesis of many acute and chronic diseases. Results from animal and human studies suggest that dysbiosis is linked to cardiovascular and metabolic disease through changes to microbiota-derived metabolites, including trimethylamine-N-oxide and short-chain fatty acids. Dysbiosis can occur within hours of surgery or the onset of critical illness, even without the administration of antibiotics. These pathological changes in microbiota may contribute to important clinical outcomes, including surgical infection, bowel anastomotic leaks, acute kidney injury, respiratory failure and brain injury. As a strategy to reduce dysbiosis, the use of probiotics (live bacterial cultures that confer health benefits) or synbiotics (probiotic in combination with food that encourages the growth of gut commensal bacteria) in surgical and critically ill patients has been increasingly reported to confer important clinical benefits, including a reduction in ventilator-associated pneumonia, bacteraemia and length of hospital stay, in small randomised controlled trials. However, the best strategy to modulate dysbiosis or counteract its potential harms remains uncertain and requires investigation by a well-designed, adequately powered, randomised controlled trial.

Antimicrobial de-escalation as part of antimicrobial stewardship in intensive care: no simple answers to simple questions-a viewpoint of experts

Antimicrobial de-escalation (ADE) is defined as the discontinuation of one or more components of combination empirical therapy, and/or the change from a broad-spectrum to a narrower spectrum antimicrobial. It is most commonly recommended in the intensive care unit (ICU) patient who is treated with broad-spectrum antibiotics as a strategy to reduce antimicrobial pressure of empirical broad-spectrum therapy and prevent antimicrobial resistance, yet this has not been convincingly demonstrated in a clinical setting. Even if it appears beneficial, ADE may have some unwanted side effects: it has been associated with prolongation of antimicrobial therapy and could inappropriately be used as a justification for unrestricted broadness of empirical therapy. Also, exposing a patient to multiple, sequential antimicrobials could have unwanted effects on the microbiome. For these reasons, ADE has important shortcomings to be promoted as a quality indicator for appropriate antimicrobial use in the ICU. Despite this, ADE clearly has a role in the management of infections in the ICU. The most appropriate use of ADE is in patients with microbiologically confirmed infections requiring longer antimicrobial therapy. ADE should be used as an integral part of an ICU antimicrobial stewardship approach in which it is guided by optimal specimen quality and relevance. Rapid diagnostics may further assist in avoiding unnecessary initiation of broad-spectrum therapy, which in turn will decrease the need for subsequent ADE.

Impact of Human Microbiome on Health

The human genome in the recent years, by the advent of technological advancements, has emerged as a major prolocutor for reciprocity between the human body and the food consumed. As known, microbiome comprises all the genetic materials within a microbiota and can thereby be also referred to as metagenome of the microbiota. Contemporary researches have revealed the influence of microbiome not only on human mind and health status, but also in wide range of disease switching, ranging from cardio-metabolic diseases, allergies and obesities to life-threatening diseases such as cancer. Though the complete mechanism of many diseases is yet unclear, research works have revealed that the metabolites, nutrients and microbes can be regarded as the key players for such physiological state. The major approach of this chapter is to enlighten the interrelationship of the microbiome on the human health either in a synergistic or in an antagonistic manner.

Urinary Oxalate Excretion and Long-Term Outcomes in Kidney Transplant Recipients

Epidemiologic studies have linked urinary oxalate excretion to risk of chronic kidney disease (CKD) progression and end-stage renal disease. We aimed to investigate whether urinary oxalate, in stable kidney transplant recipients (KTR), is prospectively associated with risk of graft failure. In secondary analyses we evaluated the association with post-transplantation diabetes mellitus, all-cause mortality and specific causes of death. Oxalate excretion was measured in 24-h urine collection samples in a cohort of 683 KTR with a functioning allograft ≥1 year. Mean eGFR was 52 ± 20 mL/min/1.73 m2. Median (interquartile range) urinary oxalate excretion was 505 (347-732) µmol/24-h in women and 519 (396-736) µmol/24-h in men (p = 0.08), with 302 patients (44% of the study population) above normal limits (hyperoxaluria). A consistent and independent inverse association was found with all-cause mortality (HR 0.77, 95% CI 0.63-0.94, p = 0.01). Cause-specific survival analyses showed that this association was mainly driven by an inverse association with mortality due to infection (HR 0.56, 95% CI 0.38-0.83, p = 0.004), which remained materially unchanged after performing sensitivity analyses. Twenty-four-hour urinary oxalate excretion did not associate with risk of graft failure, post-transplant diabetes mellitus, cardiovascular mortality, mortality due to malignancies or mortality due to miscellaneous causes. In conclusion, in KTR, 24-h urinary oxalate excretion is elevated in 44% of KTR and inversely associated with mortality due to infectious causes.

Antimicrobial de-escalation in critically ill patients: a position statement from a task force of the European Society of Intensive Care Medicine (ESICM) and European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Critically Ill Patients Study Group (ESGCIP)

BACKGROUND

Antimicrobial de-escalation (ADE) is a strategy of antimicrobial stewardship, aiming at preventing the emergence of antimicrobial resistance (AMR) by decreasing the exposure to broad-spectrum antimicrobials. There is no high-quality research on ADE and its effects on AMR. Its definition varies and there is little evidence-based guidance for clinicians to use ADE in the intensive care unit (ICU).

METHODS

A task force of 16 international experts was formed in November 2016 to provide with guidelines for clinical practice to develop questions targeted at defining ADE, its effects on the ICU population and to provide clinical guidance. Groups of 2 experts were assigned 1-2 questions each within their field of expertise to provide draft statements and rationale. A Delphi method, with 3 rounds and an agreement threshold of 70% was required to reach consensus.

RESULTS

We present a comprehensive document with 13 statements, reviewing the evidence on the definition of ADE, its effects in the ICU population and providing guidance for clinicians in subsets of clinical scenarios where ADE may be considered.

CONCLUSION

ADE remains a topic of controversy due to the complexity of clinical scenarios where it may be applied and the absence of evidence to the effects it may have on antimicrobial resistance.

Drug-Induced Small Bowel Injury: a Challenging and Often Forgotten Clinical Condition

PURPOSE OF REVIEW

Most drugs are given by the oral route. Oral intake allows direct contact between the drug and the entire GI tract mucosa, exposing it to potential topical damage until absorption. Medication-induced GI symptoms and lesions are therefore commonly encountered in clinical practice. This review will examine the most common drugs or classes of drugs affecting small bowel function and/or structure.

RECENT FINDINGS

Since non-steroidal anti-inflammatory drugs (NSAIDs) are among the most widely used medicines, NSAID enteropathy is highly prevalent and brings about considerable morbidity. Antimicrobials and proton-pump inhibitors profoundly modify intestinal microbiota, affecting gut sensory and motor functions, while other drugs (like iron and gold derivatives) impair intestinal permeability. Olmesartan (and likely ACE inhibitors) induce villous atrophy and consequent malabsorption. Mycophenolate mofetil, cancer chemotherapeutic agents, and immune checkpoint inhibitors cause intestinal inflammation, abdominal pain, and diarrhea. Potassium chloride supplements may induce small bowel ulceration, stenosis, and perforation while the cotraceptive pill and anticoagulants are associated with intestinal ischemia and spontaneous intramural hematoma, respectively. In clinical practice, a deep knowledge of clinical pharmacology and toxicology and a high degree of suspicion of drug-related adverse events are mandatory. Only then, the practicing physician will be able to diagnose medication-induced small bowel lesions correctly and will implement the best strategies to treat them.