Detection of thermotolerant coliforms and SARS-CoV-2 RNA in sewage and recreational waters in the Ecuadorian coast: A call for improving water quality regulation.

Wastewater surveillance represents an alternative approach to regulating contamination and the early detection of infectious agents and outbreaks of diseases of public health importance. This study evaluated domestic wastewater effects on recreational waters in estuarine and seawater bodies in Guayas and Santa Elena provinces in Ecuador, South America. Fecal indicator bacteria (thermotolerant coliforms) served as key indicators for evaluation. Physical, chemical, and microbiological quality markers following the Ecuadorian environmental quality standard and the discharge of effluents to the water resource were analyzed. Samples were collected from 44 coastal sites and 2 oxidation lagoons during the dry and rainy seasons of 2020 and 2021, respectively. SARS-CoV-2 RNA was detected in samples with higher E. coli concentrations using reverse transcription quantitative PCR to detect the genes N and ORF1ab. All samples analyzed for SARS-CoV-2 showed Ct ˂ 40 for at least one gene. Four samples showed at least 20 genome copies of gene N per reaction. These were at an artisanal fishing port, an estuarine area (Palmar), a recreational bay, and an oxidation lagoon. A moderate correlation was found between SARS-CoV-2 RNA, thermotolerant coliform and E. coli (p-value ≤ 0.0037), and a strong and positive correlation between thermotolerant coliform and E. coli. (p-value ≤ 0.00001), highlighting the utility of these established parameters as a proxy of the virus. Significant differences were found in the concentrations of thermotolerant coliforms between seasons (p-value = 0.016) and sites (p-value = 0.005). The highest levels of coliforms were found in the dry season (63000 MPN/100 mL) in Anconcito and during the rainy season (14000 MPN/100 mL) at Esterillo in Playas County. It is recommended that the decentralized autonomous governments of the surveyed provinces in Ecuador implement urgent corrective actions and establish medium-term mechanisms to minimize a potential contamination route. Additional parameters must be included in the monitoring, such as Enterococcus and intestinal parasites, due to their public health implications. In the oxidation lagoons, maintenance actions must be carried out, including the dissolution of sediments, an increase in water retention times, and in situ treatment of the sludge, to improve the system's performance.

Multiple anthropogenic stressors in the Galápagos Islands' complex social-ecological system: Interactions of marine pollution, fishing pressure, and climate change with management recommendations.

For decades, multiple anthropogenic stressors have threatened the Galápagos Islands. Widespread marine pollution such as oil spills, persistent organic pollutants, metals, and ocean plastic pollution has been linked to concerning changes in the ecophysiology and health of Galápagos species. Simultaneously, illegal, unreported, and unregulated fishing are reshaping the composition and structure of endemic and native Galápagos pelagic communities. In this novel review, we discuss the impact of anthropogenic pollutants and their associated ecotoxicological implications for Galápagos species in the face of climate change stressors. We emphasize the importance of considering fishing pressure and marine pollution, in combination with climate-change impacts, when assessing the evolutionary fitness of species inhabiting the Galápagos. For example, the survival of endemic marine iguanas has been negatively affected by organic hydrocarbons introduced via oil spills, and endangered Galápagos sea lions exhibit detectable concentrations of DDT, triggering potential feminization effects and compromising the species' survival. During periods of ocean warming (El Niño events) when endemic species undergo nutritional stress, climate change may increase the vulnerability of these species to the impacts of pollutants, resulting in the species reaching its population tipping point. Marine plastics are emerging as a deleterious and widespread threat to endemic species. The Galápagos is treasured for its historical significance and its unparalleled living laboratory and display of evolutionary processes; however, this unique and iconic paradise will remain in jeopardy until multidisciplinary and comprehensive preventative management plans are put in place to mitigate and eliminate the effects of anthropogenic stressors facing the islands today. We present a critical analysis and synthesis of anthropogenic stressors with some progress from local and international institutional efforts and call to action more precautionary measures along with new management philosophies focused on understanding the processes of change through research to champion the conservation of the Galápagos. Integr Environ Assess Manag 2023;19:870-895. © 2022 SETAC.

Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada.

Although numerous studies have detected SARS-CoV-2 RNA in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 RNA and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 RNA in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 RNA in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 RNA concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in 15.27 ± 3.32% recovery of an internal positive control, Armored RNA, and a high positivity rate of SARS-CoV-2 RNA in stored wastewater samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids in fresh wastewater samples. Our results suggested that SARS-CoV-2 RNA may predominate in solids, and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 RNA was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 RNA was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 RNA concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 RNA loads in wastewater.

Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.

Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a syndrome of unknown etiology characterized by profound fatigue exacerbated by physical activity, also known as post-exertional malaise (PEM). Previously, we did not detect evidence of immune dysregulation or virus reactivation outside of PEM periods. Here we sought to determine whether cardiopulmonary exercise stress testing of ME/CFS patients could trigger such changes. ME/CFS patients (n = 14) and matched sedentary controls (n = 11) were subjected to cardiopulmonary exercise on 2 consecutive days and followed up to 7 days post-exercise, and longitudinal whole blood samples analyzed by RNA-seq. Although ME/CFS patients showed significant worsening of symptoms following exercise versus controls, with 8 of 14 ME/CFS patients showing reduced oxygen consumption ([Formula: see text]) on day 2, transcriptome analysis yielded only 6 differentially expressed gene (DEG) candidates when comparing ME/CFS patients to controls across all time points. None of the DEGs were related to immune signaling, and no DEGs were found in ME/CFS patients before and after exercise. Virome composition (P = 0.746 by chi-square test) and number of viral reads (P = 0.098 by paired t-test) were not significantly associated with PEM. These observations do not support transcriptionally-mediated immune cell dysregulation or viral reactivation in ME/CFS patients during symptomatic PEM episodes.

RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.

Background: Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In a previous study, we described similar clinical phenotypes in CFS patients and alternatively diagnosed chronic Lyme syndrome (ADCLS) patients­individuals diagnosed with Lyme disease by testing from private Lyme specialty laboratories but who test negative by reference 2-tiered serologic analysis. Methods: Here, we performed blinded RNA-seq analysis of whole blood collected from 25 adults diagnosed with CFS and 13 ADCLS patients, comparing these cases to 25 matched controls and 11 patients with well-controlled systemic lupus erythematosus (SLE). Samples were collected at patient enrollment and not during acute symptom flares. RNA-seq data were used to study host gene expression, B-cell/T-cell receptor profiles (BCR/TCR), and potential viral infections. Results: No differentially expressed genes (DEGs) were found to be significant when CFS or ADCLS cases were compared to controls. Forty-two DEGs were found when SLE cases were compared to controls, consistent with activation of interferon signaling pathways associated with SLE disease. BCR/TCR repertoire analysis did not show significant differences between CFS and controls or ADCLS and controls. Finally, viral sequences corresponding to anelloviruses, human pegivirus 1, herpesviruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) across all genus-level taxonomic categories. Conclusions: Our observations do not support a theory of transcriptionally mediated immune cell dysregulation in CFS and ADCLS, at least outside of periods of acute symptom flares.

Abundance of class 1-3 integrons in South Carolina estuarine ecosystems under high and low levels of anthropogenic influence.

The impact of human activity on the spread of antibiotic resistant bacteria throughout coastal estuarine ecosystems is not well characterized. It has been suggested that laterally transferred genetic agents, such as integrons, play a role in the spread of resistant bacteria throughout ecosystems. This study compares the distribution of three integron classes throughout a coastal estuarine ecosystem. To determine integron distribution patterns, DNA was extracted from sediment and water collected at seven sites throughout two estuaries with different levels of anthropogenic input and integrons analyzed using quantitative PCR. The data show that while all three integron classes are present, the relative abundance is different, with class 2 integrons significantly elevated in areas of high anthropogenic input and class 1 integrons elevated in areas of low input. Our results provide a foundation for using integron gene distribution as a biomarker of urban impact on antibiotic resistance gene flow and ecosystem health.

Characterization and quantitation of a novel ß-lactamase gene found in a wastewater treatment facility and the surrounding coastal ecosystem.

Wastewater treatment plants (WWTPs) are engineered structures that collect, concentrate, and treat human waste, ultimately releasing treated wastewater into local environments. While WWTPs efficiently remove most biosolids, it has been shown that many antibiotics and antibiotic-resistant bacteria can survive the treatment process. To determine how WWTPs influence the concentration and dissemination of antibiotic-resistant genes into the environment, a functional metagenomic approach was used to identify a novel antibiotic resistance gene within a WWTP, and quantitative PCR (qPCR) was used to determine gene copy numbers within the facility and the local coastal ecosystem. From the WWTP metagenomic library, the fosmid insert contained in one highly resistant clone (MIC, ≈ 416 µg ml(-1) ampicillin) was sequenced and annotated, revealing 33 putative genes, including a 927-bp gene that is 42% identical to a functionally characterized ß-lactamase from Staphylococcus aureus PC1. Isolation and subcloning of this gene, referred to as bla(M-1), conferred ampicillin resistance to its Escherichia coli host. When normalized to volume, qPCR showed increased concentrations of bla(M-1) during initial treatment stages but 2-fold-decreased concentrations during the final treatment stage. The concentration ng(-1) DNA increased throughout the WWTP process from influent to effluent, suggesting that bla(M-1) makes up a significant proportion of the overall genetic material being released into the coastal ecosystem. Average discharge was estimated to be 3.9 × 10(14) copies of the bla(M-1) gene released daily into this coastal ecosystem. Furthermore, the gene was observed in all sampled coastal water and sediment samples surrounding the facility. Our results suggest that WWTPs may be a pathway for the dissemination of novel antibiotic resistance genes into the environment.

Acute effects of the antibiotic oxytetracycline on the bacterial community of the grass shrimp, Palaemonetes pugio.

The toxicity of oxytetracycline (OTC) was evaluated in adult grass shrimp, Palaemonetes pugio. Initially, static acute (96 h) toxicity tests were conducted with shrimp exposed from 0 to 1,000 mg/L OTC. A calculated lethal concentration 50% value of 683.30 mg/L OTC (95% confidence interval 610.85-764.40 mg/L) was determined from these tests, along with a lowest-observable-effect concentration of 750 mg/L and no-observable-effect concentration of 500 mg/L. Moreover, chronic sublethal effects of OTC exposure on grass shrimp intestinal bacterial population were assessed using doses from 0 to 32 mg/L OTC. The total viable counts in digestive tract content had levels between 5.2 and 1x10(4) colony-forming units per gram of tissue at times 0 and 96 h, respectively. Aeromonas hydrophila were the most resistant isolates (27.78%) to OTC exposure. Vibrio alginolyticus showed significant positive growth following exposure to OTC, whereas other bacterial species abundance declined over time. A total of 268 bacterial isolates were screened using antibiotic resistance analysis from a library containing 459 isolates. Among the tested isolates from the OTC treatments, 15.4% were resistant to OTC and 84.6% were OTC sensitive. Oxytetracycline was generally not consistently quantifiable with liquid chromatography-mass spectroscopy technique in shrimp homogenates. The only peak detected was at the 32 mg/L dose of OTC at 96 h. Nevertheless, OTC had a significant biological effect on the bacterial population. Antibiotic resistance to five other antibiotics (penicillin G, sulfathiazole, trimethoprim, trimethoprim and sulfamethoxazole, and tetracycline) was strongly associated with OTC exposures. The present study indicates that OTC toxicity effects in P. pugio and changes in the shrimp microbial community would only be expected under special circumstances.