Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.

Gaps in communication between different staff groups and older adult patients foster unnecessary antibiotic prescribing for urinary tract infections in hospitals: a qualitative translation approach.

Background: Studies have reported large scale overprescribing of antibiotics for urinary tract infection (UTI) in hospitalised older adults. Older adults often have asymptomatic bacteriuria, and clinicians have been found to diagnose UTIs inappropriately based on vague symptoms and positive urinalysis and microbiology. However, the joined perspectives of different staff groups and older adult patients on UTI diagnosis have not been investigated. Methods: Thematic analysis of qualitative interviews with healthcare staff (n = 27) and older adult patients (n = 14) in two UK hospitals. Results: Interviews featured a recurrent theme of discrepant understandings and gaps in communication or translation between different social groups in three key forms: First, between clinicians and older adult patients about symptom recognition. Second, between nurses and doctors about the use and reliability of point-of-care urinary dipsticks. Third, between nurses, patients, microbiologists and doctors about collection of urine specimens, contamination of the specimens and interpretation of mixed growth laboratory results. The three gaps in communication could all foster inappropriate diagnosis and antibiotic prescribing. Conclusion: Interventions to improve diagnosis and prescribing for UTIs in older adults typically focus on educating clinicians. Drawing on the sociological concept of translation and interviews with staff and patients our findings suggest that inappropriate diagnosis and antibiotic prescribing in hospitals can be fuelled by gaps in communication or translation between different staff groups and older adult patients, using different languages and technologies or interpreting them differently. We suggest that interventions in this area may be improved by also addressing discrepant understandings and communication about symptoms, urinary dipsticks and the process of urinalysis.

The potential of visible blue light (405 nm) as a novel decontamination strategy for carbapenemase-producing enterobacteriaceae (CPE).

Background: Carbapenemase-producing Enterobacteriaceae (CPE) pose a considerable threat to modern medicine. New treatment options and methods to limit spread need to be investigated. Blue light (BL) is intrinsically antimicrobial, and we have previously demonstrated significant antimicrobial effects on biofilms of a panel of isolates, including two CPEs.This study was performed to assess the antibacterial activity of 405 nm BL against a panel of CPE isolates (four encoding blaNDM, three blaKPC, two blaOXA-48, and three encoding both NDM and OXA-48 carbapenemases). Methods: In vitro experiments were conducted on 72 h old biofilms of CPEs which were exposed to 60 mW/cm2 of BL. Changes to biofilm seeding were assessed by measuring the optical density of treated and untreated biofilms. Results: Twelve bacterial clinical isolates (comprising eight Klebsiella pnemoniae, one K. oxytoca, and three Escherichia coli) were tested. BL was delivered for 5, 15 and 30 min, achieving doses of 162, 54, and 108 J/cm2, respectively.All of the CPEs were susceptible to BL treatment, with increasing reductions in seeding with increasing durations of exposure. At 30 min, reductions in biofilm seeding of ≥80% were observed for 11 of the 12 isolates, compared to five of 12 after 15 min. CPE_8180 was less susceptible than the rest, with a maximum reduction in seeding of 66% at 30 min. Conclusions: BL is effective at reducing the seeding of mature CPE biofilms in vitro, and offers great promise as a topical decontamination/treatment agent for both clinical and environmental applications.

A systematic review of quantitative burn wound microbiology in the management of burns patients.

BACKGROUND: The early diagnosis of infection or sepsis in burns are important for patient care. Globally, a large number of burn centres advocate quantitative cultures of wound biopsies for patient management, since there is assumed to be a direct link between the bioburden of a burn wound and the risk of microbial invasion. Given the conflicting study findings in this area, a systematic review was warranted. METHODS: Bibliographic databases were searched with no language restrictions to August 2015. Study selection, data extraction and risk of bias assessment were performed in duplicate using pre-defined criteria. Substantial heterogeneity precluded quantitative synthesis, and findings were described narratively, sub-grouped by clinical question. RESULTS: Twenty six laboratory and/or clinical studies were included. Substantial heterogeneity hampered comparisons across studies and interpretation of findings. Limited evidence suggests that (i) more than one quantitative microbiology sample is required to obtain reliable estimates of bacterial load; (ii) biopsies are more sensitive than swabs in diagnosing or predicting sepsis; (iii) high bacterial loads may predict worse clinical outcomes, and (iv) both quantitative and semi-quantitative culture reports need to be interpreted with caution and in the context of other clinical risk factors. CONCLUSION: The evidence base for the utility and reliability of quantitative microbiology for diagnosing or predicting clinical outcomes in burns patients is limited and often poorly reported. Consequently future research is warranted.

Antibacterial Activity of Blue Light against Nosocomial Wound Pathogens Growing Planktonically and as Mature Biofilms.

UNLABELLED: The blue wavelengths within the visible light spectrum are intrinisically antimicrobial and can photodynamically inactivate the cells of a wide spectrum of bacteria (Gram positive and negative) and fungi. Furthermore, blue light is equally effective against both drug-sensitive and -resistant members of target species and is less detrimental to mammalian cells than is UV radiation. Blue light is currently used for treating acnes vulgaris and Helicobacter pylori infections; the utility for decontamination and treatment of wound infections is in its infancy. Furthermore, limited studies have been performed on bacterial biofilms, the key growth mode of bacteria involved in clinical infections. Here we report the findings of a multicenter in vitro study performed to assess the antimicrobial activity of 400-nm blue light against bacteria in both planktonic and biofilm growth modes. Blue light was tested against a panel of 34 bacterial isolates (clinical and type strains) comprising Acinetobacter baumannii, Enterobacter cloacae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae, and Elizabethkingia meningoseptica All planktonic-phase bacteria were susceptible to blue light treatment, with the majority (71%) demonstrating a ≥5-log10 decrease in viability after 15 to 30 min of exposure (54 J/cm(2) to 108 J/cm(2)). Bacterial biofilms were also highly susceptible to blue light, with significant reduction in seeding observed for all isolates at all levels of exposure. These results warrant further investigation of blue light as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications. IMPORTANCE: Blue light shows great promise as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications (e.g., wound closure during surgery). This warrants further investigation.

Emergence of linezolid resistance in hepatobiliary infections caused by Enterococcus faecium.

Enterococcal infections are common in liver transplantation and hepatopancreaticobiliary (HPB) surgery. Linezolid is frequently used to treat not only vancomycin-resistant Enterococcus (VRE), but also vancomycin-sensitive Enterococcus (VSE) infections, and resistance can develop. This study evaluated all the Liver Unit patients who developed infections with linezolid-resistant Enterococcus (LRE) in order to elicit the association with prior linezolid usage, to explore possible risk factors for infection, and to better understand the epidemiology of these isolates in this patient group. Between 2010 and 2015, infections with LRE developed in 10 patients (8 following liver transplantation and 2 following HPB surgery) after 22-108 days of treatment. Selected pulsed-field gel electrophoresis demonstrated that 2 out of 10 patients were cocolonized with different strains and indicated that cross-transmission may have occurred. In conclusion, in this group of patients with complex hepatobiliary infections, the optimal antibiotic strategies for the treatment of Enterococcus faecium infections are not clearly defined, and there is a significant risk of emergence of resistance to linezolid in E. faecium after exposure to this agent in patients, especially in the presence of a deep source of infection on a background of hepatic artery insufficiency. Caution is needed when using prolonged courses of linezolid in this setting, and further studies are necessary to determine the optimum treatment.

Protocol for a systematic review of quantitative burn wound microbiology in the management of burns patients.

BACKGROUND: Sepsis from burn injuries can result from colonisation of burn wounds, especially in large surface area burns. Reducing bacterial infection will reduce morbidity and mortality, and mortality for severe burns can be as high as 15 %. There are various quantitative and semi-quantitative techniques to monitor bacterial load on wounds. In the UK, burn wounds are typically monitored for the presence or absence of bacteria through the collection and culture of swabs, but no absolute count is obtained. Quantitative burn wound culture provides a measure of bacterial count and is gaining increased popularity in some countries. It is however more resource intensive, and evidence for its utility appears to be inconsistent. This systematic review therefore aims to assess the evidence on the utility and reliability of different quantitative microbiology techniques in terms of diagnosing or predicting clinical outcomes. METHODS/DESIGN: Standard systematic review methods aimed at minimising bias will be employed for study identification, selection and data extraction. Bibliographic databases and ongoing trial registers will be searched and conference abstracts screened. Studies will be eligible if they are prospective studies or systematic reviews of burn patients (any age) for whom quantitative microbiology has been performed, whether it is compared to another method. Quality assessment will be based on quality assessment tools for diagnostic and prognostic studies and tailored to the review as necessary. Synthesis is likely to be primarily narrative, but meta-analysis may be considered where clinical and methodological homogeneity exists. DISCUSSION: Given the increasing use of quantitative methods, this is a timely systematic review, which will attempt to clarify the evidence base. As far as the authors are aware, it will be the first to address this topic. TRIAL REGISTRATION: PROSPERO, CRD42015023903.

The Antibacterial Activity of Acetic Acid against Biofilm-Producing Pathogens of Relevance to Burns Patients.

INTRODUCTION: Localised infections, and burn wound sepsis are key concerns in the treatment of burns patients, and prevention of colonisation largely relies on biocides. Acetic acid has been shown to have good antibacterial activity against various planktonic organisms, however data is limited on efficacy, and few studies have been performed on biofilms. OBJECTIVES: We sought to investigate the antibacterial activity of acetic acid against important burn wound colonising organisms growing planktonically and as biofilms. METHODS: Laboratory experiments were performed to test the ability of acetic acid to inhibit growth of pathogens, inhibit the formation of biofilms, and eradicate pre-formed biofilms. RESULTS: Twenty-nine isolates of common wound-infecting pathogens were tested. Acetic acid was antibacterial against planktonic growth, with an minimum inhibitory concentration of 0.16-0.31% for all isolates, and was also able to prevent formation of biofilms (at 0.31%). Eradication of mature biofilms was observed for all isolates after three hours of exposure. CONCLUSIONS: This study provides evidence that acetic acid can inhibit growth of key burn wound pathogens when used at very dilute concentrations. Owing to current concerns of the reducing efficacy of systemic antibiotics, this novel biocide application offers great promise as a cheap and effective measure to treat infections in burns patients.

Antimicrobial dressings: Comparison of the ability of a panel of dressings to prevent biofilm formation by key burn wound pathogens.

UNLABELLED: Antimicrobial medicated dressings (AMD) are often used to reduce bacterial infection of burns and other wounds. However, there is limited literature regarding comparative efficacies to inform effective clinical decision making. OBJECTIVES: Following on from a previous study where we demonstrated good antibiofilm properties of acetic acid (AA), we assessed and compared the in vitro anti-biofilm activity of a range of AMDs and non-AMDs to AA. METHODS: Laboratory experiments determined the ability of a range of eleven commercial AMD, two nAMD, and AA, to prevent the formation of biofilms of a panel of four isolates of Pseudomonas aeruginosa and Acinetobacter baumannii. RESULTS: There is a large variation in ability of different dressings to inhibit biofilm formation, seen between dressings that contain the same, and those that contain other antimicrobial agents. The best performing AMD were Mepilex(®) Ag and Acticoat. AA consistently prevented biofilm formation. CONCLUSIONS: Large variation exists in the ability of AMD to prevent biofilm formation and colonisation of wounds. A standardised in vitro methodology should be developed for external parties to examine and compare the efficacies of commercially available AMDs, along with robust clinical randomised controlled trials. This is essential for informed clinical decision-making and optimal patient management.

A multi-centre comparison of nursing staff time required for the preparation and administration of liposomal amphotericin B and amphotericin B deoxycholate vs. voriconazole.

AIMS AND OBJECTIVES: To compare the nursing time and cost required for preparation and administration of liposomal amphotericin B, amphotericin B deoxycholate and voriconazole. DESIGN: Cost comparison study. METHODS: Nurse activities associated with the preparation and administration of the three study drugs were divided into 11 tasks and timed by observers at five hospitals. Target tasks were defined as those likely to be affected by the differences between drugs and excluded those tasks likely to differ owing to site-specific factors. Mean times for administration of a single day of therapy for each study drug were compared. Costs of preparation and administration of a 14-day regimen were estimated. RESULTS: Sixty-nine patients were observed receiving a total of 256 doses of study medications. Labour times were 20, 16, 14 and 3 minutes per day for liposomal amphotericin B, amphotericin B deoxycholate, intravenous voriconazole and oral voriconazole, respectively. Administration time was significantly lower for intravenous voriconazole compared with liposomal amphotericin B (p < 0.05), and for oral voriconazole compared with all intravenous regimens (p < 0.05). Preparation of medications took the longest time for intravenous formulations and was longer for liposomal amphotericin B than for the other drugs by 3-5 minutes. Average non-drug costs associated with preparation and administration of a 14-day regimen were greatest in the amphotericin B deoxycholate arm at US$ 335, followed by liposomal amphotericin B (US$ 310) and voriconazole (US$ 180). CONCLUSION: Intravenous voriconazole required less time to prepare and administer on a daily basis than liposomal amphotericin B, and was similar to amphotericin B deoxycholate. Measurements of intravenous vs. oral voriconazole administration suggest the opportunity to save 10-17 minutes per day with the oral formulation. RELEVANCE TO CLINICAL PRACTICE: Oral voriconazole may provide significant savings in terms of nursing time compared with intravenous antifungal drugs.

A study of the relationship between environmental contamination with methicillin-resistant Staphylococcus aureus (MRSA) and patients' acquisition of MRSA.

OBJECTIVE: The study aimed to examine the presence of methicillin-resistant Staphylococcus aureus (MRSA) in the environment and its relationship to patients' acquisition of MRSA. DESIGN: A prospective study was conducted in a 9-bed intensive care unit for 14 months. At every environmental screening, samples were obtained from the same 4 sites in each bed space. Patients were screened at admission and then 3 times weekly. All environmental and patient strains were typed using pulsed-field gel electrophoresis. RESULTS: MRSA was isolated from the environment at every environmental screening, when both small and large numbers of patients were colonized. Detailed epidemiological typing of 250 environmental and 139 patient isolates revealed 14 different pulsed-field gel electrophoresis profiles, with variants of EMRSA-15 being the predominant type. On only 20 (35.7%) of 56 occasions were the strains isolated from the patients and the strains isolated from their immediate environment indistinguishable. There was strong evidence to suggest that 3 of 26 patients who acquired MRSA while in the intensive care unit acquired MRSA from the environment. CONCLUSIONS: This study reveals widespread contamination of the hospital environment with MRSA, highlights the complexities of the problem of contamination, and confirms the need for more-effective cleaning of the hospital environment to eliminate MRSA.

Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains.

Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.