Genome and metabolome ms-based mining of a marine strain of Aspergillus affinis

Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis’s strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, L-pyroglutamic acid, lecanoric acid), antifungal (e.g., L-pyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati.SUPPLEMENTARY MATERIAL : Table S1: Gene annotation, Table S2: Carbohydrate active enzymes prediction, Table S3: Secreted proteins, Table S4: Transporter’s prediction, Table S5: Biosynthetic Gene Clusters, Table S6: Summary of genomic features of Circumdati genomes, Table S7: Comparison of CAZymes families between A. affinis CMG 70 and ATCC MYA-4773, Table S8: Full list of compounds, Table S9: List of the significantly differential compounds, File S1: matched spectral library compounds.The authors acknowledge financial support from the Portuguese Foundation for Science and Technology (FCT) to CESAM (UIDB/50017/2020+UIDP/50017/2020), Marta Tacão (CEECIND/00977/2020) and the PhD grants of M. Gonçalves (SFRH/BD/129020/2017) and S. Hilário (SFRH/BD/137394/2018).https://www.mdpi.com/journal/jofam2022BiochemistryGeneticsMicrobiology and Plant Patholog

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status

Seasonal and spatial variability of free-living bacterial community composition along an estuarine gradient (Ria de Aveiro, Portugal)

We examined the dynamics of the free-living bacterial community in the Ria de Aveiro estuary (Portugal) using 16S rDNA PCR e denaturing gradient gel electrophoresis (DGGE). Samples were collected along the salinity gradient in April, July and October 2003 and January 2004. Analysis of DGGE profiles indicated that the compositional shifts within this community occurred between the brackish and freshwater sections. Those shifts were particularly evident in samples collected in April, October and January. Less pronounced changes were also detected along the salinity gradient in the marine and brackish sections. Seasonally driven changes in microbial community in this estuary also occur. Canonical correspondence analysis (CCA) revealed that salinity and temperature accounted for a significant amount of the variability in the bacterioplank- ton community composition (26%). Dominant phylotypes were identified either by direct sequencing or by cloning and sequencing DGGE bands. Analysis of DNA sequences revealed that the dominant bacterial groups changed from Bacteroidetes, Alpha-proteobacteria and Gamma-proteobacteria in the marine-brackish section to Bacteroidetes, Beta-proteobacteria, Delta-proteobacteria and Epsilon-proteobacteri a in the freshwater section of the estuary

Effects of exposure to biomass burning on pulmonary inflammatory markers and pulmonary function in individuals with COPD

Introduction: Pulmonary rehabilitation (PR) has many benefits for individuals with COPD. However, it is not clear whether PR could prevent the hazards of air pollution exposure. This study aimed to analyze the effects of biomass burning exposure on pulmonary inflammatory markers and pulmonary function in individuals with COPD, participants and non-participants of PR. Methods: 35 subjects were divided into three groups: individuals with COPD who received PR (G1, n = 15), those who did not (G2, n = 10), and a control group composed of healthy individuals without COPD (CG, n = 10). Measurements of lung function and concentrations of IL-6, IL-10, and TNF-α in exhaled breath condensate samples were collected. The assessment and concentrations of particulate matter (PM10), nitrogen dioxide (NO2), ozone (O3), temperature (T), and relative air humidity (RAH) were recorded in biomass burning and non-burning periods. Results: There was a significant increase in the concentrations of air pollutants in the biomass burning period. In this period, an increase in IL-6 (G1p = 0.041, G2 p = .012), and a reduction in the FEV1/FVC ratio (G1p = 0.021, G2 p = .007) were observed in individuals with COPD. In G1, the increase in IL-6 concentrations correlated positively with O3 (r = 0.693; p = .006), and negatively with RAH (r = â0.773; p = .003) in the burning period. Conclusions: Individuals with COPD exposed to biomass burning demonstrated increased pulmonary inflammation and a reduction in the FEV1/FVC ratio, regardless of their engagement in PR. Keywords: COPD, Air pollution, Pulmonary inflammatory markers, Lung, Interleukins, Spirometr

Correlation between heart rate variability indexes and aerobic physiological variables in patients with COPD

Background and objectivePrevious studies have shown a relationship between the level of physical fitness and autonomic variables. However, these relationships have not been investigated in patients with chronic obstructive pulmonary disease (COPD). The objective of this study was to correlate the resting heart rate variability (HRV) indexes with aerobic physiological variables obtained at a maximal exercise test in patients with COPD.MethodsThirty-seven patients with COPD (63 (59-70) years; 46 (35.4-63.7) forced expiratory volume in 1 s (FEV1)%) underwent assessment of autonomic modulation at rest for 20min to determine the HRV indexes in time and frequency domains. Soon after that, the patients performed an incremental exercise test to determine the anaerobic threshold (GET), the peak oxygen uptake (VO2PEAK) and the velocity corresponding to VO2PEAK (vVO(2PEAK)).ResultsThe indexes that express parasympathetic component as RMSSD (11.4 [7.5-23.8], HF (ms(2)) (35 [17-195] and SD1 (8.1 [5.3-16.8]), correlated with GET (r=0.39; r=0.43; r=0.39 respectively). The indexes that represent the overall variability, SDNN (19.5 [13.9-28.8]), LF (ms(2)) (111 [38-229]), and SD2 (26.8 [18.6-35.4]) correlated with vVO(2PEAK) (r=0.37; r=0.38; r=0.37; r=0.44; r=0.43; r=0.46 respectively). Likewise, the indexes LF (ms(2)), LF (nu) (63.2 [46-77,9]), HF (nu) (36.8 [22.1-54]), and LF/HF (1.7 [0.9-3.5]) correlated with VO2PEAK (r=0.35; r=0.35; r=-0.35; r=0.40 respectively).ConclusionsThis study demonstrated that HRV indexes at rest may become a predictive tool for aerobic capacity in COPD patients after the development of more consistent methods.This study aimed to investigate whether the HRV indexes correlate with aerobic physiological variables obtained in cardiopulmonary exercise testing of patients with COPD. Such correlation would have important clinical implications as it would allow, prior to the realization of the maximal exercise testing, to infer the patient's aerobic capacity.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Validated predictive modelling of the environmental resistome.

Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmental resistome.The ISME Journal advance online publication, 13 February 2015; doi:10.1038/ismej.2014.237

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status