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

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

A paleolimno-metagenomic exploration of Lake Constance sediments : Ancient DNA records of environmental change

During the 20th century, many lakes of the Northern Hemisphere were affected by increasing human population and urbanisation along their shorelines and in their catchment areas, leading to, for example, eutrophication. Ecosystem monitoring commenced only after these changes became apparent, precluding any examination of timing and dynamics of the initial community change and of comparisons of the pre- and post-impact communities. With improving DNA extraction and sequencing methods, historical changes in lake communities can now be examined through DNA of organisms that have been living in the past, which is archived in lake sediments. Peri-Alpine Lake Constance (Germany), which underwent a well-documented, mid-century period of eutrophication followed by re-oligotrophication, and which is now experiencing warmer temperatures, was chosen as a model system in this study. Sediment cores with of up to 73 cm in length, reaching back to the early 18th century, were taken from different basins and sites of Lake Constance and analysed for the deposited sedimentary DNA (sedDNA). I focussed on plankton organisms, such as algae and other protists, cyanobacteria, Fungi and parasitic protists, and on aquatic plants as well as on the terrestrial vegetation along the shorelines and catchment area. This was done by PCR-amplicon sequencing using four genetic markers that reconstructed the aquatic microbial eukaryote (18S rRNA gene fragment), diatom (rbcL fragment), cyanobacteria (cyanobacteria-specific 16S rRNA gene fragment) and plant communities (trnL intron fragment) across the different sediment cores from Upper and Lower Lake Constance. For ecological inferences, the relative read abundances and overall diversity, i.e., alpha and beta diversities, were analysed for each group, and their temporal responses were examined in relation to environmental change, in particular the phosphorus loading of Lake Constance. A general trend reconstructed by the sedDNA-analyses was that a higher alpha diversity was observed in the deeper and, thus, older sediment layers, from where an overall loss of diversity was indicated towards younger sediment layers, independent of the sampling sites. All groups,with exception of diatoms showed an earlier and stronger community shift relative to the strong eutrophication phase of the 1950s: break points with loss of diversity were detected for the microbial eukaryote and cyanobacteria biomarkers as early as in the 1920s and for the terrestrial plant community as early as the 1900s. Diatoms, which are traditionally used as paleolimnologic proxies due to their microfossils, showed the latest response in the sedDNA analyses. In addition, for the 1990s, the microbial eukaryote, cyanobacteria and diatom markers each indicated another break point, towards increasing diversity, which corresponded to the increasing re-oligotrophication of Lake Constance by that time. Accordingly, a strong correlation between the community changes and the phosphorus loading of Lake Constance was indicated for these markers. The different plankton-markers showed furthermore that the overall diversity values after re-oligotrophication reverted to values similar to those of the pre-eutrophic phase, but that their present community composition is significantly different. This suggested that the ecosystem Lake Constance has not reverted back to the initial community, i.e., was not reversible, but that it is changing further. A significant correlation of climate warming with community change in the recent times could be demonstrated for the cyanobacteria and for both terrestrial and aquatic-plants. In addition, analyses show temporal congruency among specific taxonomic groups and interactions between them suggested an increased influence of biotic interactions from the 1970s onwards - independent of the physicochemical-abiotic stressor; however, this needs to be confirmed with further analyses. For the changes of the terrestrial-plant community starting at around 1900, a high correlation with human land-use change and with individual historical events was detected. These included the building of the island Reichenau dam and the subsequent planting of Populus trees, as well as meteorological events such as major flooding and extensive freezing of the lake. In addition, a shift in the plant community towards plants with economic value was detectable. The aquatic plant community for comparison showed a much lower degree of diversity change by sedDNA-analysis. In conclusion, with these studies I successfully analysed sedDNA from physiologically and phylogenetically divergent uni- and multi-cellular organisms from sediment cores taken from multiple sites across Lake Constance. I was able to reconstruct the historical perturbations of these communities on a centennial timescale and thereby their response to natural and anthropogenic changes. The inferences discussed in this thesis not only pave the way to a more comprehensive understanding of the aquatic and terrestrial community dynamics within and around a large and heterogeneous aquatic system such as Lake Constance, but also highlight the potential of using sedDNA metabarcoding for long-term environmental monitoring.publishe

Heterogeneity across Neotropical aquatic environments affects prokaryotic and eukaryotic biodiversity based on environmental DNA

Characterizing biological communities and knowledge on the distribution of biodiversity allows the assessment of ecological quality. This provides valuable information for conservation biology and monitoring purposes. While obtaining such data has been challenging in the past, environmental DNA (eDNA) sampling represents a promising tool to describe biodiversity on a broad taxonomic scale. In this study, we provide the first broad-scale biodiversity assessment for ten Neotropical water bodies in Nicaragua (a major river, two great lakes, and seven relatively young and small crater lakes) using eDNA sampling to determine how abiotic factors structure the distribution of prokaryotic and eukaryotic biodiversity across these environments. Further, we explored to what extent levels of biodiversity are associated across different taxonomic groups and environments. We found that prokaryotic and eukaryotic α-diversity was consistently higher in the great lakes (i.e., Lakes Nicaragua and Managua) as well as in Río San Juan compared with the young and small crater lakes. Differences of prokaryotic and eukaryotic communities (β-diversity) were significantly correlated, indicating that biological communities are similarly structured across environments. Accordingly, differences in salinity were correlated with prokaryotic and eukaryotic communities, whereas differences in dissolved oxygen were only correlated with prokaryotic communities (β-diversity). Yet, salinity and dissolved oxygen only affected prokaryotic α-diversity, suggesting different effects of these two abiotic factors on biodiversity within aquatic environments. Moreover, α-diversity of different phyla was positively correlated, although more strongly in prokaryotes, showing that biodiversity patterns are congruent across a broad range of lineages, particularly in prokaryotes.publishe

Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA

During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships

Image Defogging Framework Using Segmentation and the Dark Channel Prior

Foggy images suffer from low contrast and poor visibility problem along with little color information of the scene. It is imperative to remove fog from images as a pre-processing step in computer vision. The Dark Channel Prior (DCP) technique is a very promising defogging technique due to excellent restoring results for images containing no homogeneous region. However, having a large homogeneous region such as sky region, the restored images suffer from color distortion and block effects. Thus, to overcome the limitation of DCP method, we introduce a framework which is based on sky and non-sky region segmentation and restoring sky and non-sky parts separately. Here, isolation of the sky and non-sky part is done by using a binary mask formulated by floodfill algorithm. The foggy sky part is restored by using Contrast Limited Adaptive Histogram Equalization (CLAHE) and non-sky part by modified DCP. The restored parts are blended together for the resultant image. The proposed method is evaluated using both synthetic and real world foggy images against state of the art techniques. The experimental result shows that our proposed method provides better entropy value than other stated techniques along with have better natural visual effects while consuming much lower processing time

The Urology Residency Program in Israel—Results of a Residents Survey and Insights for the Future

Objective Urology practice has undergone several changes in recent years mainly related to novel technologies introduced. We aimed to get the residents’ perspective on the current residency program in Israel and propose changes in it. Methods A web-based survey was distributed among urology residents. Results 61 residents completed the survey out of 95 to whom it was sent (64% compliance). A total of 30% replied that the 9 months of mandatory general surgery rotation contributed to their training, 48% replied it should be shortened/canceled, and 43% replied that the Step A exam (a mandatory written certifying exam) in general surgery was relevant to their training. A total of 37% thought that surgical exposure during the residency was adequate, and 28% considered their training “hands-on.” Most non-junior residents (post-graduate year 3 and beyond) reported being able to perform simple procedures such as circumcision and transurethral resections but not complex procedures such as radical and laparoscopic procedures. A total of 41% of non-junior residents practice at a urology clinic. A total of 62% of residents from centers with no robotics replied its absence harmed their training, and 85% replied they would benefit from a robotics rotation. A total of 61% of residents from centers with robotics replied its presence harmed their training, and 72% replied they would benefit from an open surgery rotation. A total of 82% of the residents participated in post-graduate courses, and 81% replied they would engage in a clinical fellowship. Conclusion Given the survey results we propose some changes to be considered in the residency program. These include changes in the general surgery rotation and exam, better surgical training, possible exchange rotations to expose residents to robotic and open surgery (depending on the availability of robotics in their center), greater out-patient urology clinic exposure, and possible changes in the basic science period

Prevalence of central sleep apnea among veterans and response rate to continuous positive airway pressure therapy.

STUDY OBJECTIVES: Sleep-disordered breathing (SDB) is common in the Veteran population. In this retrospective study, we investigated the prevalence of comorbid central and obstructive SDB and the response rate to PAP among Veterans. METHODS: Veterans were screened from a single VA medical center who had polysomnography (PSG) study from 2017 to 2021 to ascertain the presence, severity, and type of SDB by measuring the apnea-hypopnea index (AHI) and central apnea index (CAI). Patients were excluded if they did not have complete studies (diagnostic and PAP titration studies). The inclusion criteria for these analyses were central sleep apnea (CSA) defined as AHI ≥ 10 events/hour and CAI ≥ 5 events/hour. Diagnostic CSA only was defined as AHI ≥ 10 events/hour and CAI ≥ 50% of AHI. OSA only was defined if AHI ≥ 10 events/hour and CAI &lt; 5 events/hour. Comorbid central and obstructive sleep apnea (COSA) was defined if AHI ≥ 10 events/hour and CAI &gt; 5 events/hour but &lt; 50% of AHI. The responsiveness to PAP therapy was determined based on the CAI &lt; 5 events/hour on the titration study. RESULTS: A total of 90 patients met the inclusion criteria and from those 64 Veterans were found to have COSA (71%), 18 (20%) were CSA only, and 8 (9%) were OSA only. A total of 22 (24.4%) Veterans diagnosed with CSA or COSA were responsive to PAP therapy. Sixty days after treatment initiation, both responsive and nonresponsive groups had significant decreases in AHI and CAI (p &lt; 0.05). CONCLUSIONS: Comorbid central and obstructive SDB is common among Veterans. The response to PAP therapy is suboptimal but improves over time