An update on gastrointestinal endoscopy-associated infections and their contributing factors

Introduction

During clinical use, gastrointestinal endoscopes are grossly contaminated with patient’s native flora. These endoscopes undergo reprocessing to prevent infectious transmission upon future use. Endoscopy-associated infections and outbreaks have been reported, with a recent focus on the transmission of multi-drug resistant organisms. This review aims to provide an update on endoscopy-associated infections, and the factors contributing to their occurrence.

Methods

PubMed, ScienceDirect, and CINAHL were searched for articles describing gastrointestinal endoscopy-associated infections and outbreaks published from 2008 to 2018. Factors contributing to their occurrence, and the outcomes of each outbreak were also examined.

Results

This review found 18 articles, 16 of which described duodenoscope-associated infections, and the remaining two described colonoscope- and gastroscope-associated infection respectively. Outbreaks were reported from the United States, France, China, Germany, the Netherlands and the United Kingdom. The causative organisms reported were Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli and Salmonella enteritidis.

Conclusions

A number of factors, including lapses in reprocessing, biofilm formation, endoscope design issues and endoscope damage, contribute to gastrointestinal endoscopy associated infection. Methods of improving endoscope reprocessing, screening for contamination and evaluating endoscope damage may be vital to preventing future infections and outbreaks.

     

The effects of care bundles on patient outcomes: a systematic review and meta-analysis

Background

Care bundles are a set of three to five evidence-informed practices performed collectively and reliably to improve the quality of care. Care bundles are used widely across healthcare settings with the aim of preventing and managing different health conditions. This is the first systematic review designed to determine the effects of care bundles on patient outcomes and the behaviour of healthcare workers in relation to fidelity with care bundles.

Methods

This systematic review is reported in line with the PRISMA statement for reporting systematic reviews and meta-analyses. A total of 5796 abstracts were retrieved through a systematic search for articles published between January 1, 2001, to February 4, 2017, in the Cochrane Central Register for Controlled Trials, MEDLINE, EMBASE, British Nursing Index, CINAHL, PsychInfo, British Library, Conference Proceeding Citation Index, OpenGrey trials (including cluster-randomised trials) and non-randomised studies (comprising controlled before-after studies, interrupted time series, cohort studies) of care bundles for any health condition and any healthcare settings were considered. Following the removal of duplicated studies, two reviewers independently screen 3134 records. Three authors performed data extraction independently. We compared the care bundles with usual care to evaluate the effects of care bundles on the risk of negative patient outcomes. Random-effect models were used to further explore the effects of subgroups.

Results

In total, 37 studies (6 randomised trials, 31 controlled before-after studies) were eligible for inclusion. The effect of care bundles on patient outcomes is uncertain. For randomised trial data, the pooled relative risk of negative effects between care bundle and control groups was 0.97 [95% CI 0.71 to 1.34; 2049 participants]. The relative risk of negative patient outcomes from controlled before-after studies favoured the care bundle treated groups (0.66 [95% CI 0.59 to 0.75; 119,178 participants]). However, using GRADE, we assessed the certainty of all of the evidence to be very low (downgraded for risk of bias, inconsistency, indirectness).

Conclusions

Very low quality evidence from controlled before-after studies suggests that care bundles may reduce the risk of negative outcomes when compared with usual care. By contrast, the better quality evidence from six randomised trials is more uncertain.

Trial registration

PROSPERO, CRD42016033175

     

Delay in diagnosis of pulmonary tuberculosis in low-and middle-income settings: systematic review and meta-analysis

Background

Assessment of delays in seeking care and diagnosis of tuberculosis is essential to evaluate effectiveness of tuberculosis control programs, and identify programmatic impediments. Thus, this review of studies aimed to examine the extent of patient, health system, and total delays in diagnosis of pulmonary tuberculosis in low- and middle- income countries.

Methods

It was done following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Electronic databases were searched to retrieve studies published from 2007 to 2015 including Pubmed central, Springer link, Hinari and Google scholar. Searching terms were pulmonary tuberculosis, health care seeking, health care seeking behavior, patient delay, diagnostic delay, health system delay, provider delay, and doctor delay. Retrieved studies were systematically reviewed and summarized using Comprehensive Meta-analysis software.

Results

Forty studies involving 18,975 patients qualified for systematic review, and 14 of them qualified for meta-analysis. The median diagnostic delay ranged from 30 to 366.5 days [IQR?=?44–77.8], with a 4–199 days [IQR?=?15–50] and 2–128.5 days [IQR?=?12–34] due to patient and health system delays, respectively. The meta-analysis showed 42% of pulmonary tuberculosis patients delayed seeking care by a month or more; uneducated patients [pooled OR?=?1.5, 95%CI?=?1.1–1.9] and those who sought initial care from informal providers [pooled OR?=?3, 95%CI?=?2.3–3.9] had higher odds of patient delay.

Conclusion

Delay in diagnosis is still a major challenge of tuberculosis control and prevention programs in low- and middle- income settings. Efforts to develop new strategies for better case-finding using the existing systems and improving patients’ care seeking behavior need to be intensified.

     

Short- and long-term outcomes in infective endocarditis patients: a systematic review and meta-analysis

Background

Despite advances in medical knowledge, technology and antimicrobial therapy, infective endocarditis (IE) is still associated with devastating outcomes. No reviews have yet assessed the outcomes of IE patients undergoing short- and long-term outcome evaluation, such as all-cause mortality and IE-related complications. We conducted a systematic review and meta-analysis to examine the short- and long-term mortality, as well as IE-related complications in patients with definite IE.

Methods

A computerized systematic literature search was carried out in PubMed, Scopus and Google Scholar from 2000 to August, 2016. Included studies were published studies in English that assessed short-and long-term mortality for adult IE patients. Pooled estimations with 95% confidence interval (CI) were calculated with DerSimonian-Laird (DL) random-effects model. Sensitivity and subgroup analyses were also performed. Publication bias was evaluated using inspection of funnel plots and statistical tests.

Results

Twenty five observational studies (retrospective, 14; prospective, 11) including 22,382 patients were identified. The overall pooled mortality estimates for IE patients who underwent short- and long-term follow-up were 20% (95% CI: 18.0–23.0, P?<?0.01) and 37% (95% CI: 27.0–48.0, P?<?0.01), respectively. The pooled prevalence of cardiac complications in patients with IE was found to be 39% (95%CI: 32.0–46.0) while septic embolism and renal complications accounted for 25% (95% CI: 20.0–31) and 19% (95% CI: 14.0–25.0) (all P?<?0.01), respectively.

Conclusion

Irrespective of the follow-up period, a significantly higher mortality rate was reported in IE patients, and the burden of IE-related complications were immense. Further research is needed to assess the determinants of overall mortality in IE patients, as well as well-designed observational studies to conform our results.

     

What implementation interventions increase cancer screening rates? a systematic review

Background

Appropriate screening may reduce the mortality and morbidity of colorectal, breast, and cervical cancers. However, effective implementation strategies are warranted if the full benefits of screening are to be realized. As part of a larger agenda to create an implementation guideline, we conducted a systematic review to evaluate interventions designed to increase the rate of breast, cervical, and colorectal cancer (CRC) screening. The interventions considered were: client reminders, client incentives, mass media, small media, group education, one-on-one education, reduction in structural barriers, reduction in out-of-pocket costs, provider assessment and feedback interventions, and provider incentives. Our primary outcome, screening completion, was calculated as the overall median post-intervention absolute percentage point (PP) change in completed screening tests.

Methods

Our first step was to conduct an iterative scoping review in the research area. This yielded three relevant high-quality systematic reviews. Serving as our evidentiary foundation, we conducted a formal update. Randomized controlled trials and cluster randomized controlled trials, published between 2004 and 2010, were searched in MEDLINE, EMBASE and PSYCHinfo.

Results

The update yielded 66 studies new eligible studies with 74 comparisons. The new studies ranged considerably in quality. Client reminders, small media, and provider audit and feedback appear to be effective interventions to increase the uptake of screening for three cancers. One-on-one education and reduction of structural barriers also appears effective, but their roles with CRC and cervical screening, respectively, are less established. More study is required to assess client incentives, mass media, group education, reduction of out-of-pocket costs, and provider incentive interventions.

Conclusion

The new evidence generally aligns with the evidence and conclusions from the original systematic reviews. This review served as the evidentiary foundation for an implementation guideline. Poor reporting, lack of precision and consistency in defining operational elements, and insufficient consideration of context and differences among populations are areas for additional research.

     

An outbreak vector-host epidemic model with spatial structure: the 2015–2016 Zika outbreak in Rio De Janeiro

Background

A deterministic model is developed for the spatial spread of an epidemic disease in a geographical setting. The disease is borne by vectors tosusceptible hosts through criss-cross dynamics. The model is focused on an outbreak that arises from a small number of infected hosts imported into a subregion of the geographical setting. The goal is to understand how spatial heterogeneity of the vector and host populations influences the dynamics of the outbreak, in both the geographical spread and the final size of the epidemic.

Methods

Partial differential equations are formulated to describe the spatial interaction of the hosts and vectors. The partial differential equations have reaction-diffusion terms to describe the criss-cross interactions of hosts and vectors. The partial differential equations of the model are analyzed and proven to be well-posed. A local basic reproduction number for the epidemic is analyzed.

Results

The epidemic outcomes of the model are correlated to the spatially dependent parameters and initial conditions of the model. The partial differential equations of the model are adapted to seasonality of the vector population, and applied to the 2015–2016 Zika seasonal outbreak in Rio de Janeiro Municipality in Brazil.

Conclusions

The results for the model simulations of the 2015–2016 Zika seasonal outbreak in Rio de Janeiro Municipality indicate that the spatial distribution and final size of the epidemic at the end of the season are strongly dependent on the location and magnitude of local outbreaks at the beginning of the season. The application of the model to the Rio de Janeiro Municipality Zika 2015–2016 outbreak is limited by incompleteness of the epidemic data and by uncertainties in the parametric assumptions of the model.

     

Citrate usage in the leading causes of blindness: new possibilities for the old metabolite

Introduction

Citrate is an old metabolite which is best known for the role in the Krebs cycle. Citrate is widely used in many branches of medicine. In ophthalmology citrate is considered as a therapeutic agent and an useful diagnostic tool—biomarker.

Objectives

To summarize the published literature on citrate usage in the leading causes of blindness and highlight the new possibilities for this old metabolite.

Methods

We conducted a systematic search of the scientific literature about citrate usage in ophthalmology up to January 2018. The reference lists of identified articles were searched for providing in-depth information.

Results

This systematic review included 30 articles. The role of citrate in the leading causes of blindness is presented.

Conclusions

Citrate might help inhibit cataract progression, in case of questions confirm glaucoma diagnosis or improve cornea repair treatment as adjuvant agent (therapy of ulcerating cornea after alkali injury, crosslinking procedure). However, the knowledge about possible citrate usage in ophthalmology is not widely known. Promoting recent scientific knowledge about citrate usage in ophthalmology may not only benefit of medical improvement but may also limit economic costs caused by leading causes of blindness. Further studies on citrate usage in ophthalmology should continuously be the field of scientific interest.

     

A systematic review of metabolomics biomarkers for Bisphenol A exposure

Introduction

Bisphenol A (BPA), 2,2-bis(4-hydroxyphenyl) propane, a common industrial chemical which has extremely huge production worldwide, is ubiquitous in the environment. Human have high risk of exposing to BPA and the health problems caused by BPA exposure have aroused public concern. However, the biomarkers for BPA exposure are lacking. As a rapidly developing subject, metabolomics has accumulated a large amount of valuable data in various fields. The secondary application of published metabolomics data could be a very promising field for generating novel biomarkers whilst further understanding of toxicity mechanisms.

Objectives

To summarize the published literature on the use of metabolomics as a tool to study BPA exposure and provide a systematic perspectives of current research on biomarkers screening of BPA exposure.

Methods

We conducted a systematic search of MEDLINE (PubMed) up to the end of June 25, 2017 with the key term combinations of ‘metabolomics’, ‘metabonomics’, ‘mass spectrometry’, ‘nuclear magnetic spectroscopy’, ‘metabolic profiling’ and ‘amino acid profile’ combined with ‘BPA exposure’. Additional articles were identified through searching the reference lists from included studies.

Results

This systematic review included 15 articles. Intermediates of glycolysis, Krebs cycle, β oxidation of long chain fatty acids, pentose phosphate pathway, nucleoside metabolism, branched chain amino acid metabolism, aromatic amino acids metabolism, sulfur-containing amino acids metabolism were significantly changed after BPA exposure, suggesting BPA had a highly complex toxic effects on organism which was consistent with existing studies. The biomarkers most consistently associated with BPA exposure were lactate and choline.

Conclusion

Existing metabolomics studies of BPA exposure present heterogeneous findings regarding metabolite profile characteristics. We need more evidence from target metabolomics and epidemiological studies to further examine the reliability of these biomarkers which link to low, environmentally relevant, exposure of BPA in human body.

     

Echocardiographic findings associated with mortality or transplant in patients with pulmonary arterial hypertension: A systematic review and meta-analysis

Background

Identification of patients at risk of deterioration is essential to guide clinical management in pulmonary arterial hypertension (PAH). This study aims to provide a comprehensive overview of well-investigated echocardiographic findings that are associated with clinical deterioration in PAH.

Methods

MEDLINE and EMBASE databases were systematically searched for longitudinal studies published by April 2015 that reported associations between echocardiographic findings and mortality, transplant or clinical worsening. Meta-analysis using random effect models was performed for echocardiographic findings investigated by four or more studies. In case of statistical heterogeneity a sensitivity analysis was conducted.

Results

Thirty-seven papers investigating 51 echocardiographic findings were included. Meta-analysis of univariable hazard ratios (HRs) and sensitivity analysis showed that presence of pericardial effusion (pooled HR 1.70; 95?% CI 1.44–1.99), right atrial area (pooled HR 1.71; 95?% CI 1.38–2.13) and tricuspid annular plane systolic excursion (TAPSE; pooled HR 1.72; 95?% CI 1.34–2.20) were the most well-investigated and robust predictors of mortality or transplant.

Conclusions

This meta-analysis substantiates the clinical yield of specific echocardiographic findings in the prognostication of PAH patients in day-to-day practice. In particular, pericardial effusion, right atrial area and TAPSE are of prognostic value.

     

Global phylogenetic analysis of contemporary aleutian mink disease viruses (AMDVs)

Background

Aleutian mink disease has major economic consequences on the mink farming industry worldwide, as it causes a disease that affects both the fur quality and the health and welfare of the mink. The virus causing this disease is a single-stranded DNA virus of the genus Amdoparvovirus belonging to the family of Parvoviridae. In Denmark, infection with AMDV has largely been restricted to a region in the northern part of the country since 2001, affecting only 5% of the total Danish mink farms. However, in 2015 outbreaks of AMDV were diagnosed in all parts of the country. Initial analyses revealed that the out breaks were caused by two different strains of AMDV that were significant different from the circulating Danish strains. To track the source of these outbreaks, a major investigation of global AMDV strains was initiated.

Methods

Samples from 13 different countries were collected and partial NS1 gene was sequenced and subjected to phylogenetic analyses.

Results

The analyses revealed that AMDV exhibited substantial genetic diversity. No clear country wise clustering was evident, but exchange of viruses between countries was revealed. One of the Danish outbreaks was caused by a strain of AMDV that closely resembled a strain originating from Sweden. In contrast, we did not identify any potential source for the other and more widespread outbreak strain.

Conclusion

To the authors knowledge this is the first major global phylogenetic study of contemporary AMDV partial NS1 sequences. The study proved that partial NS1 sequencing can be used to distinguish virus strains belonging to major clusters. The partial NS1 sequencing can therefore be a helpful tool in combination with epidemiological data, in relation to outbreak tracking. However detailed information on farm to farm transmission requires full genome sequencing.

     

Choice of fluids in critically ill patients

Background

Fluids are by far the most commonly administered intravenous treatment in patient care. During critical illness, fluids are widely administered to maintain or increase cardiac output, thereby relieving overt tissue hypoperfusion and hypoxia.

Main text

Until recently, because of their excellent safety profile, fluids were not considered “medications”. However, it is now understood that intravenous fluid should be viewed as drugs. They affect the cardiovascular, renal, gastrointestinal and immune systems. Fluid administration should therefore always be accompanied by careful consideration of the risk/benefit ratio, not only of the additional volume being administered but also of the effect of its composition on the physiology of the patient. Apart from the need to constantly assess fluid responsiveness, it is also important to periodically reconsider the type of fluid being administered and the evidence regarding the relationship between specific disease states and different fluid solutions.

Conclusions

The current review presents the state of the art regarding fluid solutions and presents the existing evidence on routine fluid management of critically ill patients in specific clinical settings (sepsis, Adult Respiratory Distress Syndrome, major abdominal surgery, acute kidney injury and trauma).

     

Markov modeling in hepatitis B screening and linkage to care

Background

With up to 240 million people chronically infected with hepatitis B worldwide, including an estimated 2 million in the United States, widespread screening is needed to link the infected to care and decrease the possible consequences of untreated infection, including liver cancer, cirrhosis and death. Screening is currently fraught with challenges in both the developed and developing world. New point-of-care tests may have advantages over standard-of-care tests in terms of cost-effectiveness and linkage to care. Stochastic modeling is applied here for relative utility assessment of point-of-care tests and standard-of-care tests for screening.

Methods

We analyzed effects of point-of-care versus standard-of-care testing using Markov models for disease progression in individual patients. Simulations of large cohorts with distinctly quantified models permitted the assessment of particular screening schemes. The validity of the trends observed is supported by sensitivity analyses for the simulation parameters.

Results

Increased utilization of point-of-care screening was shown to decrease hepatitis B-related mortalities and increase life expectancy at low projected expense.

Conclusions

The results suggest that standard-of-care screening should be substituted by point-of-care tests resulting in improved linkage to care and decrease in long-term complications.

     

Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy

Background

Metabolomics has been recognized as a powerful approach for disease screening. In order to highlight potential health issues in subjects, a key factor is the possibility to compare quantitatively the metabolome of their biofluids with reference values from healthy individuals. Such efforts towards the systematic characterization of the metabolome of biofluids in perfect health conditions, far from concluded for humans, have barely begun on horses.

Objectives

The present work attempts, for the first time, to give reference quantitative values for the molecules mostly represented in the urine metabolome of horses at rest and under light training, as observable by ¹H-NMR.

Methods

The metabolome of ten trotter horses, four male and six female, ranging from 3 to 8 years of age, has been observed by ¹H-NMR spectroscopy before and after three training sessions.

Results

We could characterize and quantify 54 molecules in trotter horse urine, originated from diet, protein digestion, energy generation or gut-microbial co-metabolism.

Conclusion

We were able to describe how gender, age and exercise affected their concentration, by means of a two steps protocol based on univariate and robust principal component analysis.

     

Cytogenetic changes of mesenchymal stem cells in the neoplastic bone marrow niche in leukemia

Background

Bone marrow mesenchymal stromal cells (BM-MSCs) are an essential cell type in the hematopoietic microenvironment. The question of whether MSCs from patients with different leukemias have cytogenetic abnormalities is controversial. In this study, we attempted to review the cytogenetic profiles of MSCs in patients with leukemia, and verify whether these profiles were related to different ex vivo culture conditions or to chronic or acute disease states. This information could be useful in clarifying the origin of MSCs and developing clinical applications for this cell type.

Methods

A systematic literature search was performed using the PubMed search engine. Studies published over the past 15 years, i.e., between 1995 and January 2015, were considered for review. The following keywords were used: “cytogenetic,” “leukemia,” “bone marrow,” and “mesenchymal stromal cells.”

Results

Some studies demonstrated that BM-MSCs are cytogenetically normal, whereas others provided evidence of aberrations in these cells

Conclusions

Studying cytogenetic changes of MSCs in a variety of leukemias will help researchers understand the nature of these tumors and ensure the safety of human stem cells in clinical applications.

     

Investigation of the relationship between cell surface hydrophobicity and demulsifying capability of biodemulsifier-producing bacteria

Background

Cell surface hydrophobicity (CSH) is one of the key physicochemical features of biodemulsifier-producing bacteria that influence their demulsification capability maintenance in petroleum contaminated environments.

Methods

In present study, biodemulsifier-producing bacteria were isolated from petroleum contaminated environments using different isolation media and the correlation between their CSH and demulsifying ability was investigated. The demulsifying ability of isolates was measured through demulsification tests on water in kerosene emulsions. The microbial adhesion to the hydrocarbon (MATH) assay was used to denote their CSH.

Results

The evaluation of CSH showed that majority of biodemulsifier producing bacteria have high CSH which indicating a positive correlation between CSH and demulsifying capability.

Conclusions

According to these results it can be concluded that CSH can be used as an indicator for assessment of biodemulsifier-producing bacteria and screening of new isolates for their biodemulsifier production.

     

Measuring anterior trunk deformity in scoliosis: development of asymmetry parameters using surface topography (a pilot study)

Background

Clinicians who assess and treat patients for scoliosis typically use parameters that are all visible from the posterior view. Radiographs assess the internal spinal deformity, but do not directly evaluate body shape, either posterior or anterior. This is problematic, as the patient is most concerned about the way they appear in the mirror. An objective set of anterior measurements is needed to help quantify the anterior asymmetry that is present in scoliosis.

Methods

The design of this system of assessment was developed as a consensus of thinking from four points of view. A spine surgeon provided the musculoskeletal structural perspective. A plastic surgeon specializing in breast reconstruction provided the aesthetic and soft tissue perspective. A surface topography researcher provided the imaging perspective, and a scoliosis patient provided the self-perception and emotional perspective.Using an iterative process, a series of potential measurement parameters using surface topography measurements were considered, debated, and ultimately selected to be part of a system of measurement that provides an overall assessment of anterior trunk asymmetry.

Results

An anterior surface topography scan in the relaxed, standing position was taken of the scoliosis patient. The computer provides a 3D topographical model that is used to complete measurements that can be combined to achieve an Anterior Aesthetic Deformity Score. Shoulder parameters, including shoulder height difference and shoulder slope difference, make up 40 % of the total score. Breast asymmetry, including nipple height difference and sternal notch-to-nipple distance, make up 30 % of the total score. Waist asymmetry makes up the final 30 % of the score, providing an objective and quantifiable measure of anterior trunk deformity.

Conclusions

These measurements provide an objective, systematic evaluation of anterior trunk asymmetry that can be used in the assessment of patients with scoliosis. Clinical research should now be done to validate this system and show that it is reproducible in a variety of settings and patients.

     

Inference of genetic relatedness between viral quasispecies from sequencing data

Background

RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations.

Results

We present (i) an evolutionary simulation algorithm Viral Outbreak InferenCE (VOICE) inferring genetic relatedness, (ii) an algorithm MinDistB detecting possible transmission using minimal distances between intra-host viral populations and sizes of their relative borders, and (iii) a non-parametric recursive clustering algorithm Relatedness Depth (ReD) analyzing clusters’ structure to infer possible transmissions and their directions. All proposed algorithms were validated using real sequencing data from HCV outbreaks.

Conclusions

All algorithms are applicable to the analysis of outbreaks of highly heterogeneous RNA viruses. Our experimental validation shows that they can successfully identify genetic relatedness between viral populations, as well as infer transmission clusters and outbreak sources.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.