Building Community Consensus for Scientific Metadata with YAMZ

ABSTRACTThis paper reports on a demonstration of YAMZ (Yet Another Metadata Zoo) as a mechanism for building community consensus around metadata terms. The demonstration is motivated by the complexity of the metadata standards environment and the need for more user-friendly approaches for researchers to achieve vocabulary consensus. The paper reviews a series of metadata standardization challenges, explores crowdsourcing factors that offer possible solutions, and introduces the YAMZ system. A YAMZ demonstration is presented with members of the Toberer materials science laboratory at the Colorado School of Mines, where there is a need to confirm and maintain a shared understanding for the vocabulary supporting research documentation, data management, and their larger metadata infrastructure. The demonstration involves three key steps: 1) Sampling terms for the demonstration, 2) Engaging graduate student researchers in the demonstration, and 3) Reflecting on the demonstration. The results of these steps, including examples of the dialog provenance among lab members and voting, show the ease with YAMZ can facilitate building metadata vocabulary consensus. The conclusion discusses implications and highlights next steps

Environmental surveillance for Salmonella Typhi and its association with typhoid fever incidence in India and Malawi

Background Environmental surveillance (ES) for Salmonella Typhi potentially offers a low-cost tool to identify communities with a high burden of typhoid fever. Methods We developed standardised protocols for typhoid ES, including sampling site selection, validation, characterisation; grab or trap sample collection, concentration; and quantitative PCR targeting Salmonella genes (ttr, staG and tviB) and a marker of human faecal contamination (HF183). ES was implemented over 12-months in a historically high typhoid fever incidence setting (Vellore, India) and a lower incidence setting (Blantyre, Malawi) during 2021-2022. Results S. Typhi prevalence in ES samples was higher in Vellore compared with Blantyre; 39/520 (7.5%, 95% Confidence Interval 4.4-12.4%) vs. 11/533 (2.1%, 1.1-4.0%) in grab and 79/517 (15.3%, 9.8-23.0%) vs. 23/594 (3.9%, 1.9-7.9%) in trap samples. Detection was clustered by ES site and correlated with site catchment population in Vellore but not Blantyre. Incidence of culture-confirmed typhoid in local hospitals was low during the study and zero some months in Vellore despite S. Typhi detection in ES. Conclusions ES describes the prevalence and distribution of S. Typhi even in the absence of typhoid cases and could inform vaccine introduction. Expanded implementation and comparison with clinical and serological surveillance will further establish its public health utility

Development, confirmation, and application of a seeded Escherichia coli process control organism to validate Salmonella enterica serovar Typhi environmental surveillance methods

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of Typhoid fever. Blood culture is the gold standard for clinical diagnosis, but this is often difficult to employ in resource limited settings. Environmental surveillance of waste-impacted waters is a promising supplement to clinical surveillance, however validating methods is challenging in regions where S. Typhi concentrations are low. To evaluate existing S. Typhi environmental surveillance methods, a novel process control organism (PCO) was created as a biosafe surrogate. Using a previous described qPCR assay, a modified PCR amplicon for the staG gene was cloned into E. coli. We developed a target region that was recognized by the Typhoid primers in addition to a non-coding internal probe sequence. A multiplex qPCR reaction was developed that differentiates between the typhoid and control targets, with no cross-reactivity or inhibition of the two probes. The PCO was shown to mimic S. Typhi in lab-based experiments with concentration methods using primary wastewater: filter cartridge, recirculating Moore swabs, membrane filtration, and differential centrifugation. Across all methods, the PCO seeded at 10 CFU/mL and 100 CFU/mL was detected in 100% of replicates. The PCO is detected at similar quantification cycle (Cq) values across all methods at 10 CFU/mL (Average = 32.4, STDEV = 1.62). The PCO was also seeded into wastewater at collection sites in Vellore (India) and Blantyre (Malawi) where S. Typhi is endemic. All methods tested in both countries were positive for the seeded PCO. The PCO is an effective way to validate performance of environmental surveillance methods targeting S. Typhi in surface water

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Characterization of persistent virus-like particles in two acetate-fed methanogenic reactors.

The objective of this study was to characterize the morphology, size-distribution, concentration and genome size of virus-like particles (VLPs) in two acetate-fed Methanosaeta-dominated reactors to better understand the possible correlation between viruses and archaeal hosts. The study reactors were dominated by a single genus of acetoclastic methanogen, Methanosaeta, which was present at 6 to 13 times higher than the combined bacterial populations consisting of Proteobacteria, Firmicutes, and Bacteroidetes. Epifluorescent microscopy showed VLPs concentration of 7.1 ± 1.5 × 10(7) VLPs/ml and 8.4 ± 4.3 × 10(7) VLPs/ml in the two laboratory reactors. Observations of no detectable import of VLPs with the reactor feed combined long operational time since the last inocula were introduced suggests that the VLP populations were actively propagating in the reactors. Transmission electron microscopy images showed VLPs with morphology consistent with Siphoviridae in both reactors, and VLPs with morphologies consistent with Myoviridae in one of the reactors. The morphology, size-distribution and genome size of VLPs were distinct between reactors suggesting that unique viral populations inhabited each reactor, though the hosts of these VLPs remain unclear

Editorial: SARS-CoV-2 in water

Sanitary Engineerin

Modification of IL-6 by hypochlorous acid: effects on receptor binding and possible role in treatment of COVID-19

Interleukin-6 (IL-6) has been implicated in the pathogenesis of acute inflammatory events in COVID-19 patients. We exposed IL-6 to hypochlorous acid (HOCl) in vitro at concentrations reported to develop in vivo. After HOCl treatment the cytokine failed to bind to IL-6 receptors in a bioassay using engineered human cells. Similar results followed exposure of IL-6 to N-chlorotaurine (NCT) and hypobromous acid (HOBr). SDS-PAGE analysis of HOCl-treated IL-6 showed neither fragmentation nor aggregation, suggesting that the modifications induced by these agents occurred on the intact protein. Mass spectrometry of intact and trypsin-digested fragments identified oxidative changes limited to two amino acid residues, methionine 161 and tryptophan 157, both of which have been implicated in receptor binding of the cytokine. Further studies on the effects of hypohalous acids and their halogenated amine derivatives on IL-6 and related cytokines is needed