Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis.

We aimed to evaluate the performance of Oxford Nanopore Technologies (ONT) sequencing from positive blood culture (BC) broths for bacterial identification and antimicrobial susceptibility prediction. Patients with suspected sepsis in four intensive care units were prospectively enrolled. Human-depleted DNA was extracted from positive BC broths and sequenced using ONT (MinION). Species abundance was estimated using Kraken2, and a cloud-based system (AREScloud) provided in silico predictive antimicrobial susceptibility testing (AST) from assembled contigs. Results were compared to conventional identification and phenotypic AST. Species-level agreement between conventional methods and AST predicted from sequencing was 94.2% (49/52), increasing to 100% in monomicrobial infections. In 262 high-quality AREScloud AST predictions across 24 samples, categorical agreement (CA) was 89.3%, with major error (ME) and very major error (VME) rates of 10.5% and 12.1%, respectively. Over 90% CA was achieved for some taxa (e.g., Staphylococcus aureus) but was suboptimal for Pseudomonas aeruginosa. In 470 AST predictions across 42 samples, with both high quality and exploratory-only predictions, overall CA, ME, and VME rates were 87.7%, 8.3%, and 28.4%. VME rates were inflated by false susceptibility calls in a small number of species/antibiotic combinations with few representative resistant isolates. Time to reporting from sequencing could be achieved within 8-16 h from BC positivity. Direct sequencing from positive BC broths is feasible and can provide accurate predictive AST for some species. ONT-based approaches may be faster but significant improvements in accuracy are required before it can be considered for clinical use.IMPORTANCESepsis and bloodstream infections carry a high risk of morbidity and mortality. Rapid identification and susceptibility prediction of causative pathogens, using Nanopore sequencing direct from blood cultures, may offer clinical benefit. We assessed this approach in comparison to conventional phenotypic methods and determined the accuracy of species identification and susceptibility prediction from genomic data. While this workflow holds promise, and performed well for some common bacterial species, improvements in sequencing accuracy and more robust predictive algorithms across a diverse range of organisms are required before this can be considered for clinical use. However, results could be achieved in timeframes that are faster than conventional phenotypic methods.

Quality of evidence supporting Surviving Sepsis Campaign Recommendations.

INTRODUCTION: The Surviving Sepsis Campaign (SSC) guidelines, released in 2017, are a combination of expert opinion and evidence-based medicine, adopted by many institutions as a standard of practice. The aim was to analyse the quality of evidence supporting recommendations on the management of sepsis. METHODS: The strength and quality of evidence (high, moderate, low-very low and best practice statements) of each recommendation were extracted. Randomised controlled trials were required to qualify as high-quality evidence. RESULTS: A total of 96 recommendations were formulated, and 87 were included. Among thirty-one (43%) strong recommendations, only 15.2% were supported by high-quality evidence. Overall, thirty-seven (42.5%) recommendations were based on low-quality evidence, followed by 28 (32.2%) based on moderate-quality, 15 (17.2%) were best practice statements and only seven (8.0%) were supported by high-quality evidence. Randomised controlled trials supported 21.4%, 9.5% and 8.6% recommendations on mechanical ventilation, resuscitation, and management/adjuvant therapy, respectively. In contrast, none high-quality evidence recommendation supported antimicrobial/source control (82.4% were low-very low evidence or best practice statements), and nutrition. CONCLUSIONS: In the SSC guidelines most recommendations were informed by indirect evidence and non-systematic observations. While awaiting trials results, Delphi-like approaches or multi-criteria decision analyses should guide recommendations.

Is inhaled prophylactic heparin useful for prevention and Management of Pneumonia in ventilated ICU patients?: The IPHIVAP investigators of the Australian and New Zealand Intensive Care Society Clinical Trials Group.

PURPOSE: To determine whether prophylactic inhaled heparin is effective for the prevention and treatment of pneumonia patients receiving mechanical ventilation (MV) in the intensive care unit. METHODS: A phase 2, double blind randomized controlled trial stratified for study center and patient type (non-operative, post-operative) was conducted in three university-affiliated intensive care units. Patients aged ≥18years and requiring invasive MV for more than 48hours were randomized to usual care, nebulization of unfractionated sodium heparin (5000 units in 2mL) or placebo nebulization with 0.9% sodium chloride (2mL) four times daily with the main outcome measures of the development of ventilator associated pneumonia (VAP), ventilator associated complication (VAC) and sequential organ failure assessment scores in patients with pneumonia on admission or who developed VAP. TRIAL REGISTRATION: Australian and New Zealand Clinical Trials Registry ACTRN12612000038897. RESULTS: Two hundred and fourteen patients were enrolled (72 usual care, 71 inhaled sodium heparin, 71 inhaled sodium chloride). There were no differences between treatment groups in terms of the development of VAP, using either Klompas criteria (6-7%, P=1.00) or clinical diagnosis (24-26%, P=0.85). There was no difference in the clinical consistency (P=0.70), number (P=0.28) or the total volume of secretions per day (P=.54). The presence of blood in secretions was significantly less in the usual care group (P=0.005). CONCLUSION: Nebulized heparin cannot be recommended for prophylaxis against VAP or to hasten recovery from pneumonia in patients receiving MV.

Meropenem versus piperacillin-tazobactam for definitive treatment of bloodstream infections due to ceftriaxone non-susceptible Escherichia coli and Klebsiella spp (the MERINO trial): study protocol for a randomised controlled trial.

BACKGROUND: Gram-negative bacteria such as Escherichia coli or Klebsiella spp. frequently cause bloodstream infections. There has been a worldwide increase in resistance in these species to antibiotics such as third generation cephalosporins, largely driven by the acquisition of extended-spectrum beta-lactamase or plasmid-mediated AmpC enzymes. Carbapenems have been considered the most effective therapy for serious infections caused by such resistant bacteria; however, increased use creates selection pressure for carbapenem resistance, an emerging threat arising predominantly from the dissemination of genes encoding carbapenemases. Recent retrospective data suggest that beta-lactam/beta-lactamase inhibitor combinations, such as piperacillin-tazobactam, may be non-inferior to carbapenems for the treatment of bloodstream infection caused by extended-spectrum beta-lactamase-producers, if susceptible in vitro. This study aims to test this hypothesis in an effort to define carbapenem-sparing alternatives for these infections. METHODS/DESIGN: The study will use a multicentre randomised controlled open-label non-inferiority trial design comparing two treatments, meropenem (standard arm) and piperacillin-tazobactam (carbapenem-sparing arm) in adult patients with bacteraemia caused by E. coli or Klebsiella spp. demonstrating non-susceptibility to third generation cephalosporins. Recruitment is planned to occur in sites across three countries (Australia, New Zealand and Singapore). A total sample size of 454 patients will be required to achieve 80% power to determine non-inferiority with a margin of 5%. Once randomised, definitive treatment will be for a minimum of 4 days, but up to 14 days with total duration determined by treating clinicians. Data describing demographic information, antibiotic use, co-morbid conditions, illness severity, source of infection and other risk factors will be collected. Vital signs, white cell count, use of vasopressors and days to bacteraemia clearance will be recorded up to day 7. The primary outcome measure will be mortality at 30 days, with secondary outcomes including days to clinical and microbiological resolution, microbiological failure or relapse, isolation of a multi-resistant organism or Clostridium difficile infection. TRIAL REGISTRATION: The MERINO trial is registered under the Australian New Zealand Clinical Trials Register (ANZCTR), reference number: ACTRN12613000532707 (registered 13 May 2013) and the US National Institute of Health ClinicalTrials.gov register, reference number: NCT02176122 (registered 24 June 2014).

Prophylaxis, empirical and preemptive treatment of invasive candidiasis.

PURPOSE OF REVIEW: Invasive candidiasis remains an important infection for ICU patients, associated with poor clinical outcomes. It has been increasingly recognized that the traditional paradigm of culture-directed antifungal treatment is unsatisfactory, and that earlier antifungal intervention strategies, such as prophylaxis, preemptive therapy, and empiric therapy, are required to improve patient outcomes. The purpose of this review is to summarize the recent supportive evidence for such strategies and to highlight the current challenges in their implementation. RECENT FINDINGS: Despite new antifungal agents and classes, the mortality from invasive candidiasis remains high. Antifungal prophylaxis remains the best-studied early antifungal intervention strategy; however, unless targeted to patients at highest risk, is inefficient. Recent data suggests that although risk predictive models, using a combination of clinical risk factors and Candida colonization parameters, may be a relatively simple and practical approach to guide prophylaxis or preemptive therapy, further validation of these models is required. A single trial has demonstrated that empiric antifungal therapy is not of benefit when instituted to patients with antibiotic-refractory fever alone. SUMMARY: On the basis of current knowledge, it is difficult to universally recommend antifungal prophylaxis, apart from patient groups with a known very high risk, such as those with necrotising pancreatitis or recurrent gastrointestinal perforations. Antifungal prophylaxis may also be reasonable where local incidence rates and epidemiology are compelling. Among stable patients with multifocal Candida colonization and/or a multitude of clinical-risk factors, preemptive therapy is currently not indicated, although the development of better risk predictive models may assist with such patients. Among patients with refractory fever despite broad-spectrum antibacterial therapy, empiric antifungal therapy may be reasonable where local incidence rates are high (e.g. >10%); however, a thorough search for alternate causes must be instituted.

Management of invasive candidiasis in the intensive care unit.

Invasive candidiasis (IC) is an important infection in the intensive care unit (ICU) setting given its association with poor clinical outcomes. The epidemiology of IC is complex and, although incompletely elucidated, is characterized by considerable regional and temporal variability. Overall, there appears to be an increase in the incidence of IC and a change in distribution of the causative Candida spp. Of particular concern is an increase in the proportion of episodes caused by Candida glabrata, which is associated with reduced susceptibility to azole antifungal agents. The management of IC has been aided by the availability of several new antifungal agents. In particular, given their broad spectrum of activity and low toxicity, the use of echinocandins as first-line therapy is increasing, especially in settings where fluconazole-resistant Candida spp. are prevalent. Fluconazole remains a reliable agent where an azole-susceptible pathogen is confirmed or in settings where resistance is uncommon. Lipid formulations of amphotericin B are now generally reserved as second-line or salvage therapy. Voriconazole and posaconazole currently enjoy limited use for IC in the ICU setting. Although the poor outcomes associated with IC are, in part, related to the severity of underlying host factors, it is clear that optimization of treatment-related factors is also important. In particular, the speed of initiation of antifungal therapy and the achievement of pharmacodynamic parameters both influence outcomes. The most difficult challenge is early initiation of an effective antifungal drug, given the slow turnaround time and lack of sensitivity of conventional culture-based diagnostic techniques. New approaches, such as non-culture-based assays and/or clinical risk-predictive models are required to better target prophylactic, pre-emptive and empirical antifungal strategies.

Antibiotic use and impact on outcome from bacteraemic critical illness: the BActeraemia Study in Intensive Care (BASIC).

BACKGROUND: The lack of prospective, randomized, controlled trial data to guide optimal antibiotic use in bacteraemic critically ill patients has led to a wide variety of strategies and major issues with drug resistance. We therefore prospectively investigated the epidemiology of bacteraemia and fungaemia in intensive care units (ICUs); and the impact of timing, type and appropriateness of antibiotic intervention. METHODS: We conducted a multinational, multicentre, prospective observational study in 132 ICUs from 26 countries with no interventions. RESULTS: 1702 patients [European (69.6%), Australasian (12.2%), South American (8.3%) and Asian (9.9%)] developed 1942 bacteraemic episodes over the study period. Mortality rates were similar for those receiving empirical (40.5%), semi-targeted (37.6%) or fully targeted (33.3%) antibiotic therapy (P=0.40), and in those initially receiving broad- (39.3%) or restricted-spectrum (39.1%) therapy (P=0.94). First-line therapy was effective in terms of the antibiogram (where available) in 70.4% of cases. This in vitro susceptibility ranged from 76.3% for broad-spectrum antibiotics to 46.3% for restricted-spectrum antibiotics (P<0.0001). However, no antibiotic policy-associated variable, including in vitro susceptibility (odds ratio 0.89, 95% confidence interval 0.61-1.30), was a statistically significant predictor of mortality. CONCLUSIONS: We could not show an impact of antibiotics on mortality in critically ill patients, despite in vitro activity and early commencement. Randomized, multicentre trials are urgently needed to establish the appropriate duration, timing and combinations of antibiotics that will both optimally treat infection and minimize development of resistance and other complications.

Measurement of tissue cortisol levels in patients with severe burns: a preliminary investigation.

INTRODUCTION: The assessment of adrenal function in critically ill patients is problematic, and there is evidence to suggest that measurement of tissue glucocorticoid activity may be more useful than estimation of plasma cortisol concentrations. Interstitial cortisol concentrations of cortisol represent the available pool of glucocorticoids able to enter the cell and bind to the glucocorticoid receptor. However the concentrations of plasma cortisol may not accurately reflect interstitial concentrations. We elected to perform a preliminary study into the feasibility of measuring interstitial cortisol by microdialysis, and to investigate the relationship between total plasma cortisol, free plasma cortisol and interstitial cortisol in patients with severe burns. METHODS: A prospective observational study carried out in a tertiary intensive care unit. Ten adult patients with a mean total burn surface area of 48% were studied. Interstitial cortisol was measured by microdialysis from patient-matched burnt and non-burnt tissue and compared with that of 3 healthy volunteers. Plasma sampling for estimations of total and free cortisol concentrations was performed concurrently. RESULTS: In the burn patients, mean total plasma and free plasma cortisol concentrations were 8.8 +/- 3.9, and 1.7 +/- 1.1 mcg/dL, (p < 0.001), respectively. Mean subcutaneous microdialysis cortisol concentrations in the burn and non-burn tissue were 0.80 +/- 0.31 vs 0.74 +/- 0.41 mcg/dL (p = 0.8), respectively, and were significantly elevated over the mean subcutaneous microdialysis cortisol concentrations in the healthy volunteers. There was no significant correlation between total plasma or free plasma and microdialysis cortisol concentrations. Plasma free cortisol was better correlated with total burn surface area than total cortisol. CONCLUSIONS: In this preliminary study, interstitial cortisol concentrations measured by microdialysis in burnt and non-burnt skin from patients with severe thermal injury are significantly elevated over those from healthy volunteers. Plasma estimations of cortisol do not correlate with the microdialysis levels, raising the possibility that plasma cortisol may be an unreliable guide to tissue cortisol activity.

Assessment of clinical risk predictive rules for invasive candidiasis in a prospective multicentre cohort of ICU patients.

PURPOSE: To assess the generalisability of published clinical risk predictive models for invasive candidiasis in ICU patients. METHODS: The performance characteristics of published clinical risk factor-only and Candida colonisation-only predictive models for invasive candidiasis were assessed in a multicentre cohort of Australian ICU patients. Clinical risk factors and Candida colonisation parameters were collected prospectively from patients. RESULTS: The two clinical risk factor-only predictive models applied to an Australian patient cohort (n = 615) performed less well than in published studies involving derivation populations. Model performance characteristics improved when Candida colonisation parameters were added post-hoc. CONCLUSIONS: Risk predictive models should factor in both clinical risk factors and Candida colonisation parameters. Integrating these models into therapeutic algorithms first requires external validation in different patient populations and settings.

Low mannose-binding lectin function is associated with sepsis in adult patients.

Mannose-binding lectin (MBL) is an innate immune system pattern recognition molecule that kills a wide range of pathogens via the lectin complement pathway. MBL deficiency is associated with severe infection but the best measure of this deficiency is undecided. We investigated the influence of MBL functional deficiency on the development of sepsis in 195 adult patients, 166 of whom had bloodstream infection and 35 had pneumonia. Results were compared with 236 blood donor controls. MBL function (C4b deposition) and levels were measured by enzyme-linked immunosorbent assay. Using receiver-operator characteristics of MBL function in healthy controls, we identified a level of <0.2 U microL(-1) as a highly discriminative marker of low MBL2 genotypes. Median MBL function was lower in sepsis patients (0.18 U microL(-1)) than in controls (0.48 U microL(-1), P<0.001). MBL functional deficiency was more common in sepsis patients than controls (P<0.001). MBL functional deficient patients had significantly higher sequential organ failure assessment (SOFA) scores and higher MBL function and levels were found in patients with SOFA scores predictive of good outcome. Deficiency of MBL function appears to be associated with bloodstream infection and the development of septic shock. High MBL levels may be protective against severe sepsis.

Effect of drug concentration on adsorption of levofloxacin by polyacrylonitrile haemofilters.

We studied an in vitro model of continuous venovenous haemofiltration to determine levofloxacin adsorption by polyacrylonitrile (PAN) filters. Four doses of levofloxacin (5, 25, 50 and 100 mg) were used, resulting in circulating concentrations of levofloxacin at 120 min of 3.56+/-0.14, 15.84+/-2.08, 31.42+/-1.95 and 58.23+/-1.10 mg/L, respectively. Adsorption at 2 h was 0.65+/-0.17, 5.99+/-2.49, 12.30+/-2.34 and 30.13+/-1.32 mg, respectively (P<0.001). From 2h to 4h, increasing the blood pump rate and the ultrafiltration rate had no effect on adsorption. When the concentration was decreased from 3.55+/-0.13 mg/L at 4h to 2.16+/-0.11 mg/L at 5 h by addition of lactated Ringer's solution, adsorption decreased from 0.67+/-0.16 mg to 0.21+/-0.25 mg (P<0.05). These data show that adsorption of levofloxacin by PAN haemofilters is concentration dependent and reversible in vitro and suggest that adsorption by haemofilters is unlikely to affect levofloxacin pharmacokinetics significantly in vivo.

The effect of adsorption, filter material and point of dilution on antibiotic elimination by haemofiltration an in vitro study of levofloxacin.

We studied an in vitro model of continuous venous-venous haemofiltration (CVVH), into which levofloxacin 100 mg was infused, to determine levofloxacin adsorption and to determine the effect of filter material and point of dilution (pre- or post-filter) on sieving coefficient. Mean (standard deviation; S.D.) adsorption was 18.7 (5.3) mg for the polyamide filter and 40.2 (2.0) mg for the polyacrylonitrile (PAN) filter (P < 0.001). Post-dilution resulted in a minor, but statistically significant, decrease in sieving coefficient (pre-dilution 0.96 (S.D. 0.10), post-dilution 0.88 (S.D. 0.11) with the PAN filter. These data indicate that the variability in published values for levofloxacin sieving coefficient are not due to variation in point of dilution or membrane type (PAN or polyamide). Significant adsorption of levofloxacin onto PAN filters occurs.

Routine changing of intravenous administration sets does not reduce colonization or infection in central venous catheters.

OBJECTIVE: To determine the effect of routine intravenous (IV) administration set changes on central venous catheter (CVC) colonization and catheter-related bacteremia. DESIGN: Prospective, randomized, controlled trial. SETTING: Eighteen-bed intensive care unit (ICU) in a large metropolitan hospital. PARTICIPANTS: Two hundred fifty-one patients with 404 chlorhexidine gluconate and silver sulfadiazine-coated multi-lumen CVCs. INTERVENTIONS: CVCs inserted in the ICU and in situ on day 4 were randomized to have their IV administration sets changed on day 4 (n = 203) or not at all (n = 201). Use of fluid containers and blood product administration sets was limited to 24 hours. CVCs were removed when not required, infection was suspected, or in place on day 7. Catheter cultures were performed on removal by blinded laboratory staff. Catheter-related bacteremia was diagnosed by a blinded intensivist using strict definitions. Data were collected regarding catheter duration, site, Acute Physiology and Chronic Health Evaluation (APACHE) II score, patient age, diagnosis, hyperglycemia, hypoalbuminemia, immune status, number of fluid containers and IV injections, and administration of propofol, blood, total parenteral nutrition, or lipid infusion. RESULTS: There were 10 colonized CVCs in the group receiving a set change and 19 in the group not receiving one. This difference was not statistically significant on Kaplan-Meier survival analysis. There were 3 cases of catheter-related bacteremia per group. Logistic regression found that burns diagnosis and increased ICU stay significantly predicted colonization. CONCLUSION: IV administration sets can be used for 7 days in patients with short-term, antiseptic-coated CVCs.

A randomised controlled study of the efficacy of hypromellose and Lacri-Lube combination versus polyethylene/Cling wrap to prevent corneal epithelial breakdown in the semiconscious intensive care patient.

OBJECTIVE: To compare the efficacy of two forms of eye care (hypromellose and Lacri-Lube combination vs polyethylene/Cling wrap covers) for intensive care patients. DESIGN: Randomised-controlled trial. SETTING: University affiliated, tertiary referral hospital. PATIENTS AND PARTICIPANTS: One hundred ten patients with a reduced or absent blink reflex were followed through until they regained consciousness, were discharged from the facility during study enrolment, died or developed a positive corneal ulcer or eye infection. INTERVENTIONS: All patients received standard eye cleansing every 2 h. In addition to this, group one ( n=60) received a treatment combining hypromellose drops and Lacri-Lube (HL) to each eye every 2 h. Group two ( n=50) had polyethylene covers only placed over the eye to create a moisture chamber. MEASUREMENTS AND RESULTS: Corneal ulceration was determined using corneal fluorescein stains and mobile slit lamp evaluation, performed daily. No patients had corneal ulceration in the polyethylene cover group, but 4 patients had corneal ulceration in the HL group. CONCLUSIONS: Polyethylene covers are as effective as HL in reducing the incidence of corneal damage in intensive care patients.

Intravascular administration sets are accurate and in appropriate condition after 7 days of continuous use: an in vitro study.

BACKGROUND: The ideal duration of intravascular administration set use is unknown. Studies have compared the infective implications of 1--7 days of use. The Centers for Disease Control recommend at least 3 days usage. No previous study has evaluated the accuracy of volume delivery or integrity of administration sets after prolonged use. AIM: To evaluate the accuracy and condition of intravascular administration sets used continuously for 7 days. DESIGN: Prospective, randomized, experimental study in the laboratory setting. METHODS: Four administration sets were randomly assigned to deliver 2 mL/hour (IMEDreg syringe set 2280--0000), 20, 50 or 100 mL/hour (IMEDreg infusion sets 2210--0500) of crystalloid solution continuously for 7 days through an IMEDreg Geminireg four channel infusion pump (PC4). At study commencement and daily for 7 days, a 4-hour volume measurement and an inspection for leaks/erosion of administration sets occurred for each administration set (total measurements = 32). RESULTS: Mean volume outputs over 4 hours were 7.84 mL (2 mL/hour), 80.66 mL (20 mL/hour), 205.35 (50 mL/hour) and 406.37 (100 mL/hour). These differed significantly from the programmed volumes (P=0.00--0.01). Usage duration did not influence performance (F=0.866, P=0.55). Accuracy of volume delivery differed significantly with pump speed (F=106.933, P < 0.001) exhibiting increased volume to 50 mL/hour then a reduction at 100 mL/hour. Differences were within manufacturer specifications (+/-5%) and were clinically acceptable. All administration sets remained in appropriate condition displaying no leakage or erosion. CONCLUSION: There were small inaccuracies found between programmed and delivered volumes, however, there was no deterioration in performance over time. This suggests that inaccuracies were because of normal pump performance rather than the administration sets. Administration sets retain acceptable accuracy and condition after 7 days continuous use. Further research should assess the infective and other impacts of prolonged usage.