Diversity of inulinase-producing fungi associated with two Asteraceous plants, Pulicaria crispa (Forssk.) and Pluchea dioscoridis (L.) growing in an extreme arid environment

Inulinases are potentially valuable enzymes catalyze the hydrolysis of plant’s inulin into high fructose syrups as sweetening ingredients for food industry and ethanol production. The high demands for inulinase enzymes have promoted interest in microbial inulinases as the most suitable approach for biosynthesis of fructose syrups from inulin. Arid land ecosystem represents a valuable bioresource for soil microbial diversity with unique biochemical and physiological properties. In the present study, we explored the fungi diversity associated with the rhizosphere and rhizoplane of two desert medicinal plants namely Pluchea dioscoridis and Pulicaria crispa growing in the South-Eastern desert of Aswan, Egypt. A total of 180 fungal isolates were screened based on their ability to grow on potato dextrose agar medium supplemented with 1% inulin. The isolated fungal colonies were morphologically identified according to cultural characteristics and spore-bearing structure. In addition, the inulinase activity of the isolated fungi was examined spectrophotometrically. Among these, Aspergillus terreus var. terreus 233, Botrytis cinerea, Aspergillus aegyptiacus, Cochliobolus australiensis 447 and Cochliobolus australiensis exhibited high inulinase activity ranging from 5.05 to 7.26 U/ml. This study provides a promising source of microbial inulinase, which can be scaled up for industrial applications. DOI: http://dx.doi.org/10.5281/zenodo.120564

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10&nbsp;years; 78.2% included were male with a median age of 37&nbsp;years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Emissions of Anaerobically Produced Methane by Trees

Recent studies indicate that plants may be a previously overlooked but significant source of atmospheric CH₄, though there is considerable disagreement on the mechanism of production. Our work sought to verify that woody deciduous trees grown under inundated conditions had the capacity for transporting CH₄ from an anaerobic subsurface to the atmosphere and to consider if such a source could be important globally. Here, we report results from a greenhouse mesocosm study that indicate significant emissions of anaerobically produced CH₄ transmitted to the atmosphere through broadleaf riparian tree species grown under flooded conditions. Using a leaf area normalized mean emission rate (0.7 ± 0.3 μg cm⁻² hr⁻¹), results were scaled globally for flooded forest regions and estimated to be 60 ± 20 Tg year⁻¹, ~10% of the global CH₄ source. The carbon isotopic composition of CH4 emitted was found to be significantly enriched compared with expectations (δ13C ~ −54‰) and provided an important isotopic constraint on the global source which coincides with the mean of the globally scaled greenhouse-based estimate

Atmospheric Methane Isotopic Record Favors Fossil Sources Flat in 1980s and 1990s with recent increase

Observations of atmospheric methane (CH4) since the late 1970s and measurements of CH4 trapped in ice and snow reveal a meteoric rise in concentration during much of the twentieth century. Since 1750, levels of atmospheric CH4 have more than doubled to current globally averaged concentration near 1,800 ppb. During the late 1980s and 1990s, the CH4 growth rate slowed substantially and was near or at zero between 1999 and 2006. There is no scientific consensus on the drivers of this slowdown. Here, we report measurements of the stable isotopic composition of atmospheric CH4 (13C/12C and D/H) from a rare air archive dating from 1977 to 1998. Together with more modern records of isotopic atmospheric CH4, we performed a time-dependent retrieval of methane fluxes spanning 25 y (1984–2009) using a 3D chemical transport model. This inversion results in a 24 [18, 27] Tg y−1 CH4 increase in fugitive fossil fuel emissions since 1984 with most of this growth occurring after year 2000. This result is consistent with some bottom-up emissions inventories but not with recent estimates based on atmospheric ethane. In fact, when forced with decreasing emissions from fossil fuel sources our inversion estimates unreasonably high emissions in other sources. Further, the inversion estimates a decrease in biomass-burning emissions that could explain falling ethane abundance. A range of sensitivity tests suggests that these results are robust

Applicability of American College of Clinical Pharmacy (ACCP) competencies to clinical pharmacy practice in Egypt

Background: The American College of Clinical Pharmacy (ACCP) prepared clinical pharmacist competencies that have specific recommendations. Recently, many efforts to advance clinical pharmacy services in Egypt exist. The literature revealed that no country has assessed the extent of applicability of ACCP competencies in its current pharmacy practice setting. Egyptian pharmacists can provide feedback about applicability of such competencies in clinical pharmacy settings in Egypt. Objective: The objective of this study was to investigate the extent to which ACCP competencies were implemented by Egyptian clinical pharmacists and therefore evaluate development of clinical pharmacy practice in Egypt. The study also investigated factors affecting the applicability of such competencies in the current clinical pharmacy practice setting in Egypt. Methods: Four hundred and ninety-five randomly selected clinical pharmacists from several hospitals were invited to participate in a cross sectional survey using a self-administered validated questionnaire composed of 31 questions classified into six domains. This questionnaire was designed to determine the pharmacists’ perception about applicability of ACCP competencies to clinical pharmacy practice in Egypt. Results: The response rate was 64% as 317 out of 495 pharmacists completed the questionnaire. These pharmacists were categorized according to age; gender; qualifications; years of previous work experience, years since BSc. and type of hospitals they are currently working at. Analysis of data revealed the professionalism domain to have the highest percentage of acceptance among pharmacists, while the system-based care & population health domain had the lowest percentage of acceptance. Results also showed that qualifications of participants did not affect their response in three domains; “Direct Patient Care”, “Systems-based Care & Population Health” and “Continuing Professional Development” (p=0.082, 0.081, 0.060), respectively. Nevertheless, qualifications of participants did affect their response in the other three domains; “Pharmacotherapy Knowledge”, “Communication” and “Professionalism” (p<0.05). The age of pharmacists, gender, years of previous work experience, and graduation year did not affect their responses in all six domains. The type of hospital they are currently working at, though, affected their responses where, there was a highly statistically significant increase of the mean score of all domains among participants working at the NGOs/private hospitals compared to governmental hospitals (p<0.001). Conclusions: Egyptian pharmacists generally apply high percentage of ACCP competencies but the provided clinical pharmacy services need to be improved through applying the standards of best practice

Diversity of inulinase-producing fungi associated with two Asteraceous plants, Pulicaria crispa (Forssk.) and Pluchea dioscoridis (L.) growing in an extreme arid environment

Inulinases are potentially valuable enzymes catalyze the hydrolysis of plant’s inulin into high fructose syrups as sweetening ingredients for food industry and ethanol production. The high demands for inulinase enzymes have promoted interest in microbial inulinases as the most suitable approach for biosynthesis of fructose syrups from inulin. Arid land ecosystem represents a valuable bioresource for soil microbial diversity with unique biochemical and physiological properties. In the present study, we explored the fungi diversity associated with the rhizosphere and rhizoplane of two desert medicinal plants namely Pluchea dioscoridis and Pulicaria crispa growing in the South-Eastern desert of Aswan, Egypt. A total of 180 fungal isolates were screened based on their ability to grow on potato dextrose agar medium supplemented with 1% inulin. The isolated fungal colonies were morphologically identified according to cultural characteristics and spore-bearing structure. In addition, the inulinase activity of the isolated fungi was examined spectrophotometrically. Among these, Aspergillus terreus var. terreus 233, Botrytis cinerea, Aspergillus aegyptiacus, Cochliobolus australiensis 447 and Cochliobolus australiensis exhibited high inulinase activity ranging from 5.05 to 7.26 U/ml. This study provides a promising source of microbial inulinase, which can be scaled up for industrial applications. DOI: http://dx.doi.org/10.5281/zenodo.120564