Ethics guidelines for environmental epidemiologists: 2023 revision.

Recognition of the importance to environmental epidemiology of ethical and philosophical deliberation led, in 1996, to the establishment of Ethics Guidelines for the profession. In 1999, these guidelines were adopted by the International Society for Environmental Epidemiology. The guidelines were revised in 2012 and again in 2023 to ensure continued relevance to the major issues facing the field. Comprising normative standards of professional conduct, the guidelines are structured into four subsections: (1) obligations to individuals and communities who participate in research; (2) obligations to society; (3) obligations regarding funders/sponsors and employers; and (4) obligations to colleagues. Through the 2023 revision of the Ethics Guidelines, the International Society for Environmental Epidemiology seeks to ensure the highest possible standards of transparency and accountability for the ethical conduct of environmental epidemiologists engaged in research and public health practice.

Landscape of global urban environmental resistome and its association with local socioeconomic and medical status.

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

A history of the MetaSUB consortium: Tracking urban microbes around the globe.

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.

Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association.

In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications.

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

Human enteric bacteria and viruses in five wastewater treatment plants in the Eastern Cape, South Africa.

Monitoring effluents from wastewater treatment plants is important to preventing both environmental contamination and the spread of disease. We evaluated the occurrence of human enteric bacteria (faecal coliforms and Escherichia coli) and viruses (rotavirus and enterovirus) in the final effluents of five wastewater treatment plants (WWTPs) in the Eastern Cape of South Africa. Human viruses were recovered from the effluent samples with the adsorption-elution method and detected with singleplex real-time RT-PCR assays. Rotavirus was detected in several effluents samples, but no enterovirus was detected. At WWTP-C, rotavirus titre up to 105genome copies/L was observed and present in 41.7% of the samples. At WWTP-B, the virus was detected in 41.7% of samples, with viral titres up to 103genome copies/L. The virus was detected once at WWTP-E, in 9% of the samples analysed. The viral titres at WWTP-A were below the detection limit in all 25% of the 1.25L samples in which the virus was detected. Rotavirus was not observed at WWTP-D. Faecal coliform bacteria and E. coli were detected in all the WWTPs, but no correlation was established between the enteric bacteria and viruses studied. The occurrence of rotavirus in effluent samples discharged into surface waters highlights the importance of assessing viral contamination in the water sources used for domestic water use.

Assessment of the Physicochemical Qualities and Prevalence of Escherichia coli and Vibrios in the Final Effluents of Two Wastewater Treatment Plants in South Africa: Ecological and Public Health Implications.

The final effluents of two wastewater treatment plants (WWTPs) in the Eastern Cape Province of South Africa were evaluated for their physicochemical and microbiological qualities over a period of 12 months. The physicochemical parameters assessed ranged as follows both plants. The ranges of values for the physicochemical are: pH (3.9-8.6), total dissolved solids (86.50-336.3 mg/L), electrical conductivity (13.57-52.50 mS/m), temperature (13-28 °C), nitrate (0-21.73 mg/L), nitrite (0.01-0.60 mg/L), orthophosphate (1.29-20.57 mg/L), turbidity (4.02-43.20 NTU), free chlorine (0.05-7.18 mg/L), dissolve oxygen (3.91-9.60 mg/L), biochemical oxygen demand (0.1-9.0 mg/L) and chemical oxygen demand (4.67-211 mg/L). The microbiological assessment for both WWTPs revealed the presence of E. coli in counts ranging between 0 and 1.86 × 104 CFU/100 mL and Vibrio counts ranging between 0 and 9.93 × 10³ CFU/100 mL. We conclude that these WWTPs are important point sources of pollution in surface water with potential public health and ecological risks.

Incidence of human adenoviruses and Hepatitis A virus in the final effluent of selected wastewater treatment plants in Eastern Cape Province, South Africa.

BACKGROUND: Municipal effluent constitutes a large reservoir of human enteric viruses and bacteria. Contemporary monitoring practices rely on indicator bacteria, and do not test for viruses. Different viruses, including Norwalk-like viruses, Hepatitis A virus (HAV), adenoviruses, and rotaviruses, are important agents of illnesses in humans. The burden of disease caused by adenoviruses manifests as pneumonia, bronchiolitis, otitis media, conjunctivitis, and tonsillitis, whereas HAV infection can manifest as acute inflammatory diseases of the liver, fever, anorexia, malaise, nausea, and abdominal discomfort, followed by jaundice and dark urine. The public health implications of these viruses depend upon the physiological status of the wastewater microbial community. METHODS: The occurrence of human adenovirus (HAdV) and HAV was determined in the final effluents of five wastewater treatment plants (WWTPs) in the Eastern Cape, South Africa, over 12 months (September 2012-August 2013). The viruses were detected with real-time PCR, and conventional PCR was used for serotyping. RESULTS: Adenovirus was detected in effluent samples from all five WWTPs and in 64 % of the total samples, whereas HAV was not detected in any effluent sample. At WWPT-A, samples were collected from the final effluent tank (adenoviral concentrations ranged from 1.05 × 10(1) to 1.10 × 10(4) genome/L, with a 41.7 % detection rate) and the discharge point (adenoviral concentrations ranged between 1.2 × 10(1) and 2.8 × 10(4) genome/L, with a 54.5 % detection rate). At WWPT-B, HAdV was detected in 91.7 % of samples, with viral concentrations of 7.92 × 10(1)-2.37 × 10(5) genome/L. The HAdV concentrations at WWPT-C were 5.32 × 10(1)-2.20 × 10(5) genome/L, and the detection rate was 75 %. The adenoviral concentrations at WWPT-D were 1.23 × 10(3)-1.05 × 10(4) genome/L, and the detection rate was 66.7 %. At WWPT-E, the viral concentrations were 1.08 × 10(1)-5.16 × 10(4) genome/L, and the detection rate was 54.5 %. Characterization of the adenoviruses revealed HAdV serotypes 2 (1.4 %) and 41 (7.1 %), in species C and F, respectively. CONCLUSIONS: This study is the first to report the prevalence of HAdV in the final effluents of WWTPs in the Eastern Cape, South Africa. The adenoviral detection rates indicate the potential contamination of the environment, with adverse effects on public health.