The World Health Organization (WHO) classified COVID-19 as a global pandemic, with the situation ultimately requiring unprecedented measures to mitigate the effects on public health and the global economy. Although SARS-CoV-2 (the virus responsible for COVID-19) is primarily respiratory in nature, multiple studies confirmed its genetic material could be detected in the feces of infected individuals, thereby highlighting sewage as a potential indicator of community incidence or prevalence. Numerous wastewater surveillance studies subsequently confirmed detection of SARS-CoV-2 RNA in wastewater and wastewater-associated solids/sludge. However, the methods employed in early studies vary widely so it is unclear whether differences in reported concentrations reflect true differences in epidemiological conditions, or are instead driven by methodological artifacts. The current study aimed to compare the performance of virus recovery and detection methods, detect and quantify SARS-CoV-2 genetic material in two Southern Nevada sewersheds from March–May 2020, and better understand the potential link between COVID-19 incidence/prevalence and wastewater concentrations of SARS-CoV-2 RNA. SARS-CoV-2 surrogate recovery (0.34%–55%) and equivalent sample volume (0.1 mL–1 L) differed between methods and target water matrices, ultimately impacting method sensitivity and reported concentrations. Composite sampling of influent and primary effluent resulted in a ∼10-fold increase in concentration relative to corresponding grab primary effluent samples, presumably highlighting diurnal variability in SARS-CoV-2 signal. Detection and quantification of four SARS-CoV-2 genetic markers (up to ∼10 6 gene copies per liter), along with ratios of SARS-CoV-2 to pepper mild mottle virus (PMMoV), exhibited comparability with public health data for two sewersheds in an early phase of the pandemic. Finally, a wastewater model informed by fecal shedding rates highlighted the potential significance of new cases (i.e., incidence rather than prevalence) when interpreting wastewater surveillance data.

BackgroundWe sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional.ResultsWe collected all available brands of retail chicken and turkey—including conventional, “raised without antibiotic”, and organic products—every two weeks from January to December 2012. In total, E. coli was recovered from 91% of 546 turkey products tested and 88% of 1367 chicken products tested. The proportion of samples contaminated with E. coli was similar across all three production categories. Resistance prevalence varied by meat type and was highest among E. coli isolates from turkey for the majority of antibiotics tested. In general, production category had little effect on resistance prevalence among E. coli isolates from chicken, although resistance to gentamicin and multidrug resistance did vary. In contrast, resistance prevalence was significantly higher for 6 of the antibiotics tested—and multidrug resistance—among isolates from conventional turkey products when compared to those labelled organic or “raised without antibiotics”. E. coli isolates from chicken varied strongly in resistance prevalence among different brands within each production category.ConclusionThe high prevalence of resistance among E. coli isolates from conventionally-raised turkey meat suggests greater antimicrobial use in conventional turkey production as compared to “raised without antibiotics” and organic systems. However, among E. coli from chicken meat, resistance prevalence was more strongly linked to brand than to production category, which could be caused by brand-level differences during production and/or processing, including variations in antimicrobial use.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1322-5) contains supplementary material, which is available to authorized users.

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Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with HO. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with HO. The positive correlation between O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE)O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity. Using quantitative stable isotope probing of microbial RNA and DNA with HO, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.

Candida auris is an opportunistic fungal pathogen and an emerging global public health threat, given its high mortality among infected individuals, antifungal resistance, and persistence in healthcare environments. This study explored the applicability of wastewater surveillance for C. auris in a metropolitan area with reported outbreaks across multiple healthcare facilities. Influent or primary effluent samples were collected over 10 weeks from seven sewersheds in Southern Nevada. Pelleted solids were analyzed using an adapted quantitative polymerase chain reaction (qPCR) assay targeting the ITS2 region of the C. auris genome. Positive detection was observed in 72 of 91 samples (79%), with higher detection frequencies in sewersheds serving healthcare facilities involved in the outbreak (94 vs 20% sample positivity). Influent wastewater concentrations ranged from 2.8 to 5.7 log 10 gene copies per liter (gc/L), and primary clarification achieved an average log reduction value (LRV) of 1.24 ± 0.34. Presumptive negative surface water and wastewater controls were non-detect. These results demonstrate that wastewater surveillance may assist in tracking the spread of C. auris and serve as an early warning tool for public health action. These findings provide the foundation for future application of wastewater-based epidemiology (WBE) to community-or facility-level surveillance of C. auris and other high consequence, healthcare-associated infectious agents.

Most soil bacterial taxa are thought to be dormant, or inactive, yet the extent to which they synthetize new rRNA is poorly understood. We analyzed O composition of RNA extracted from soil incubated with HO and used quantitative stable isotope probing to characterize rRNA synthesis among microbial taxa. RNA was not fully labeled with O, peaking at a mean of 23.6 ± 6.8 atom percent excess (APE)O after eight days of incubation, suggesting some ribonucleotides in soil were more than eight days old. Microbial taxa varied in the degree they incorporated O into their rRNA over time and there was no correlation between the APEO of bacterial rRNA and their rRNA to DNA ratios, suggesting that the ratios were not appropriate to measure ribonucleotide synthesis. Our study indicates that, on average, 94% of soil taxa produced new rRNA and therefore were metabolically active.

This study describes wastewater concentrations of SARS-CoV-2 at seven different sampling locations in Southern Nevada (ranging from 4.2 to 8.7 log 10 gc/L) and highlights several key variables affecting those concentrations, including COVID-19 incidence, sample type, and service area population. This information is important for implementing wastewater-based epidemiology, but it also provides insight relevant to the design and regulation of potable reuse systems. Specifically, smaller systems may be more prone to influent concentration spikes that can drive enteric pathogen risk during disease outbreaks. It may be possible to leverage reactor hydraulics to achieve peak “averaging” in these scenarios, although it then becomes important to consider how elevated risks at the lower percentiles potentially offset benefits at the upper percentiles. Informed by SARS-CoV-2 concentration dynamics, the current study simulated relative risk for a hypothetical enteric pathogen. Simulated reactor hydraulics (i.e., dispersion) increased pathogen concentrations by up to 2.6 logs at lower percentiles but also decreased concentrations by up to 1.1 logs at the upper percentiles that sometimes drive public health risk. Collectively, these data highlight the importance of considering outbreak conditions, pathogen spikes, and peak “averaging” in the design and operation of treatment systems and in the development of regulatory frameworks.

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