Systematic review of wastewater surveillance of antimicrobial resistance in human populations

Objectives: We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin’s concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). Results: Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8–0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84–0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. Conclusion: Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice

Review Section : Nature/Nurture Revisited I

Biologically oriented approaches to the study of human conflict have thus far been limited largely to the study of aggression. A sample of the literature on this topic is reviewed, drawing upon four major approaches: comparative psychology, ethology (including some popularized accounts), evolutionary-based theories, and several areas of human physiology. More sophisticated relationships between so-called "innate" and "acquired" determinants of behavior are discussed, along with the proper relevance of animal behavior studies for human behavior. Unless contained in a comprehensive theory which includes social and psychological variables, biolog ically oriented theories (although often valid within their domain) offer at best severely limited and at worst highly misleading explanations of complex social conflicts. The review concludes with a list of several positive contributions of these biological approaches and suggests that social scientists must become more knowledgeable about them.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68270/2/10.1177_002200277401800206.pd

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

An inter-continental comparison between the environmental histories of two lake catchment systems in montane environments of France and South West China

Inter-continental comparisons of environmental histories can improve understanding of environmental problems and hazards, and suggest possible actions to promote adaptive capacity and resilience in communities. This article presents evidence from two discrete studies incorporating the same integrated interdisciplinary methodology that lookat montane foothill environments in France and South West China. The focus of research is on reconstructing the environmental histories of two lake catchment systems, Annecy in Haute-Savoie, France, and Erhai in Yunnan province, China. The initial findings from the comparison point to very similar sequences of an emergent flood problem in the late 17th to early 18th centuries related to upland land-use transformations of different origins that act upon longer-term sequences of environmental change. Flood problems in both catchments have been met by major engineering solutions that, whilst similar to some extent, differ in technical ingenuity. What this comparison makes clear is the importance of microvariation in environments within these catchments leading to similar, though not the same,adaptive responses to the environment. While it is clear that cultural nuances can be important causes of differences in environmental decision making, particularly in respect to choice and management options, but often the responses tend to be fairly consistent in their approaches to both environmental opportunities and problems

Human impact on the environment in the Annecy Petit Lac Catchment, Haute-Savoie: A documentary approach

It is axiomatic that mountain environments are particularly vulnerable to changes in patterns of human use, over both long and medium terms, but also over quite short periods of critical activity. This paper uses archaeological and documentary records to look at the human impact on one such montane environment, the pre-alps of Savoy, over the long-term, from pre-history up to the pre-modern period. The use and modification of landscape is estimated at the level of the Annecy Petit Lac hydrological catchment taking into account spatial differences in land use in the uplands, mid-slope and plain. Land use patterns and nutrient balance are reconstructed for specific periods in time between 1561 and 1892. Results from this study demonstrate that seven main phases of human activity have left their traces in the environmental record during the historical period through to the pre-modern period. Of these the 1730-1770s and 1840-1860s stand out as two discernible periods of heightened environmental pressures at higher altitudes, which manifest themselves as discernable lowland environmental problems, such as flooding, increased erosion and declining soil fertility

Forestry and flooding in the Annecy Petit Lac Catchment, Haute-Savoie 1700-2000

Upland environments are particularly vulnerable to the stresses of climate change. The strength and persistence of such forces are not easy to measure and hence comparison of climate impacts with anthropogenic impacts has remained problematic. This paper attempts to demonstrate the nature of human impact on forest cover and flooding in the Annecy Petit Lac Catchment in pre-Alpine Haute Savoie, France, between 1730 and 2000. Local documentary sources and a pollen record provided a detailed history of forest cover and management, making it possible to plot changes in forest cover against local and regional precipitation records, and their individual and combined impacts on flooding. A main period of large-scale, uniform and rapid deforestation in the catchment was identified in the early nineteenth century, but sub-catchment patterns of reforestation and regeneration have varied up to the present. The period of deforestation was accompanied by demographic expansion and regional scale exogenous forces, such as small scale industrial development, foreign occupation, war, caveats and laws, acting alongside local scale endogenous forces and land fragmentation, agricultural crisis, and the desire for pasture. These all produced conflict between individual needs and those of communities and resulted in localised changes in forest cover. Joint phases of deforestation and flooding are more evident in individual second order tributaries than the whole catchment, but there appears to be no obvious or simple causal link between forest cover change, climate anomalies and flooding

ERS statement on standardisation of cardiopulmonary exercise testing in chronic lung diseases

The objective of this document was to standardise published cardiopulmonary exercise testing (CPET) protocols for improved interpretation in clinical settings and multicentre research projects. This document: 1) summarises the protocols and procedures used in published studies focusing on incremental CPET in chronic lung conditions; 2) presents standard incremental protocols for CPET on a stationary cycle ergometer and a treadmill; and 3) provides patients’ perspectives on CPET obtained through an online survey supported by the European Lung Foundation. We systematically reviewed published studies obtained from EMBASE, Medline, Scopus, Web of Science and the Cochrane Library from inception to January 2017. Of 7914 identified studies, 595 studies with 26 523 subjects were included. The literature supports a test protocol with a resting phase lasting at least 3 min, a 3-min unloaded phase, and an 8-to 12-min incremental phase with work rate increased linearly at least every minute, followed by a recovery phase of at least 2–3 min. Patients responding to the survey (n=295) perceived CPET as highly beneficial for their diagnostic assessment and informed the Task Force consensus. Future research should focus on the individualised estimation of optimal work rate increments across different lung diseases, and the collection of robust normative data. © ERS 2019