Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.

MOTIVATION: Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION: The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.

EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments.

BACKGROUND: A One Health approach requires integrative research to elucidate antimicrobial resistance (AMR) in the environment and the risks it poses to human health. Research on this topic involves experts from diverse backgrounds and professions. Shortcomings exist in terms of consistent, complete, and transparent reporting in many environmental studies. Standardized reporting will improve the quality of scientific papers, enable meta-analyses and enhance the communication among different experts. In this study, we aimed to generate a consensus of reporting standards for AMR research in wastewater and related aquatic environments. METHODS: Based on a risk of bias assessment of the literature in a systematic review, we proposed a set of study quality indicators. We then used a multistep modified Delphi consensus to develop the EMBRACE-WATERS statement (rEporting antiMicroBial ResistAnCE in WATERS), a checklist of recommendations for reporting in studies of AMR in wastewater and related aquatic environments. FINDINGS: Consensus was achieved among a multidisciplinary panel of twenty-one experts in three steps. The developed EMBRACE-WATERS statement incorporates 21 items. Each item contains essential elements of high-quality reporting and is followed by an explanation of their rationale and a reporting-example. The EMBRACE-WATERS statement is primarily intended to be used by investigators to ensure transparent and comprehensive reporting of their studies. It can also guide peer-reviewers and editors in evaluation of manuscripts on AMR in the aquatic environment. This statement is not intended to be used to guide investigators on the methodology of their research. INTERPRETATION: We are hopeful that this statement will improve the reporting quality of future studies of AMR in wastewater and related aquatic environments. Its uptake would generate a common language to be used among researchers from different disciplines, thus advancing the One Health approach towards understanding AMR spread across aquatic environments. Similar initiatives are needed in other areas of One Health research.

Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review.

Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded. Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis. Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth.

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of front, which cannot be accounted for by the coarse-grained model. Such fluctuations have non-trivial effects on the wave velocity. Beyond the development of a new hybrid method, we thus conclude that birth-rate fluctuations are central to a quantitatively accurate description of invasive phenomena such as tumour growth.

The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions.

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.

Enhancement of methane production in mesophilic anaerobic digestion of secondary sewage sludge by advanced thermal hydrolysis pretreatment.

Studies on the development and evolution of anaerobic digestion (AD) pretreatments are nowadays becoming widespread, due to the outstanding benefits that these processes could entail in the management of sewage sludge. Production of sewage sludge in wastewater treatment plants (WWTPs) is becoming an extremely important environmental issue. The work presented in this paper is a continuation of our previous studies with the aim of understanding and developing the advanced thermal hydrolysis (ATH) process. ATH is a novel AD pretreatment based on a thermal hydrolysis (TH) process plus hydrogen peroxide (H2O2) addition that takes advantage of a peroxidation/direct steam injection synergistic effect. The main goal of the present research was to compare the performance of TH and ATH, conducted at a wide range of operating conditions, as pretreatments of mesophilic AD with an emphasis on methane production enhancement as a key parameter and its connection with the sludge solubilization. Results showed that both TH and ATH patently improved methane production in subsequent mesophilic BMP (biochemical methane potential) tests in comparison with BMP control tests (raw secondary sewage sludge). Besides other interesting results and discussions, a promising result was obtained since ATH, operated at temperature (115 °C), pretreatment time (5 min) and pressure (1 bar) considerably below those typically used in TH (170 °C, 30 min, 8 bar), managed to enhance the methane production in subsequent mesophilic BMP tests [biodegradability factor (fB) = cumulative CH4production/cumulative CH4production (Control) = 1.51 ± 0.01] to quite similar levels than conventional TH pretreatment [fB = 1.52 ± 0.03].

Distalización de molares superiores con el Botón Distalizador de Pretz. Policlínico Tomás Romay. 2012-2014 / Distalization of superior molars with the Pretz´s Distalizer Button. Policlinic Tomas Romay. 2012-2014

Introducción: el uso de aparatología fija para la distalización de molares, que han sufrido mesogresión, ofrece múltiples variantes. El Botón Distalizador de Pretz (BDP) se destaca por la simplicidad del aparato, su eficacia y tolerancia por parte de los pacientes. Objetivo: evaluar los cambios dentales inducidos por el BDP y determinar la magnitud de la distalización. Material y Métodos: se realizó un estudio experimental longitudinal prospectivo, para evaluación de tecnología con 11 pacientes que presentaban maloclusión Clase II de Angle, por mesogresión de los primeros molares superiores en el Policlínico Tomás Romay del 2012 al 2014, a quienes se les instaló un BDP y fueron evaluados al inicio y al final del tratamiento. Resultados: se logró una reducción de la distancia del primer molar superior al plano PTV de 4,45 mm p=0,003 y una reducción en 5,32° de la inclinación del primer molar superior con respecto al plano palatino p=0,003. La distancia entre primeros molares superiores aumentó 2.51 mm p=0,003.Conclusiones: el Botón Distalizador de Prez logra un movimiento distal significativo de los molares superiores, con una ligera extrusión e inclinación distal del molar, una disminución del resalte y el sobrepase y un aumento de la longitud del arco y de la distancia entre primeros molares superiores(AU)

Introduction: the use of fixed appliance for the distalization of molars that have suffered mesogression, offers multiple variants. Pretz´s Distalizer Button stands out for the simplicity of the apparatus, their effectiveness and tolerance on the part of the patients. Objective: to evaluate the dental changes induced by the Pretz´s Distalizer Button. Material and Methods: the study included 11 patients with Class II of Angle for mesogression of the superior molars, at "Tomas Romay" Policlinic from 2012 to 2014, to those that were installed the Pretz´s Distalizer Button and they were carried out evaluations to the beginning and the end of the treatment. Results: a reduction of the distance was achieved from the first superior molar to the plane PTV 4,45 mm; p=0,003 and a reduction in 5,32° of the inclination of the first superior molar with regard to the plane palatine p=0,003. The distance among first superior molars 2.51 mm; p=0,003 increased. Conclusions: Pretz´s Distalizer Button achieves a distal movement significant of the superior molars with a slight extrusion and distal inclination()AU)

Maqueta representativa de un punto de tratamiento especial / Representative maquette of a point of special treatment

El presente trabajo tiene como objetivos divulgar la construcción de una maqueta representativa de un punto de tratamiento especial y aspectos relacionados con la liquidación de las consecuencias del uso de las armas de exterminio en masa y de productos tóxicos industriales. Sustituye, con el empleo de la maqueta, las visitas a otras unidades con el consiguiente ahorro en consumo de recursos y tiempo del personal. En la confección de esta se produjo un gasto aproximado de $1 050,87; de esto en hombres días de trabajo fue $1 020,50 y en recursos materiales $30,37. Su tiempo de vida útil se calcula en 10 años. El costo de una clase sin la maqueta es igual a $2 063,40 en un año de proceso docente; teniendo en cuenta las clases a impartir en este tiempo, el costo ascendería a $8 253,60

Maqueta representativa de un punto de tratamiento especial / Representative maquette of a point of special treatment

El presente trabajo tiene como objetivos divulgar la construcción de una maqueta representativa de un punto de tratamiento especial y aspectos relacionados con la liquidación de las consecuencias del uso de las armas de exterminio en masa y de productos tóxicos industriales. Sustituye, con el empleo de la maqueta, las visitas a otras unidades con el consiguiente ahorro en consumo de recursos y tiempo del personal. En la confección de esta se produjo un gasto aproximado de $1 050,87; de esto en hombres días de trabajo fue $1 020,50 y en recursos materiales $30,37. Su tiempo de vida útil se calcula en 10 años. El costo de una clase sin la maqueta es igual a $2 063,40 en un año de proceso docente; teniendo en cuenta las clases a impartir en este tiempo, el costo ascendería a $8 253,60(AU)