Multidrug-resistant Enterococcus faecium strains enter the Norwegian marine environment through treated sewage

This study aimed to understand the antibiotic resistance prevalence among Enterococcus spp. from raw and treated sewage in Bergen city, Norway. In total, 517 Enterococcus spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with Enterococcus faecium as the most prevalent (n = 492) species. E. faecium strains (n = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. E. faecium strains (n = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) E. faecium strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the Enterococcus spp. strains (n = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR Enterococcus spp. strains are entering the marine environment through treated sewage.

Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples

Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.

Trend of coronavirus disease 2019 pandemic in Bengaluru, Karnataka, India

The study reports the trend of coronavirus disease 2019 (COVID-19) infection observed from 2020 to 2022 in the city of Bengaluru, Karnataka, India, across each week in relation to the corresponding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sewage positivity data and other non-COVID-19 respiratory viral infections such as influenza and respiratory syncytial virus (RSV). The data on COVID-19 cases were procured from public domains, whereas the molecular testing of sewage samples and clinical samples for influenza and RSV was performed at our unit. The pattern of sewage positivity matched the waves of COVID-19, and few sewage samples in 2021 and 2022 tested positive before the onset of clinical cases. Influenza and RSV cases were reported during the periods of low COVID-19 cases. Thus, sewage surveillance is effective in monitoring the circulating SARS-CoV-2 virus, while laboratory surveillance of SARS-CoV-2, influenza, and RSV cases is pertinent to identify the common viral etiology of respiratory infections in the community.

Prevalence of Non-Polio Enteroviruses in the Sewage of Guangzhou City, China, from 2013 to 2021

Continuous surveillance of enteroviruses (EVs) in urban domestic sewage can timely reflect the circulation of EVs in the environment and crowds, and play a predictive and early warning role in EV-related diseases. To better understand the long-term epidemiological trends of circulating EVs and EV-related diseases, we conducted a 9-year (2013 to 2021) surveillance study of non-polio EVs (NPEVs) in urban sewage in Guangzhou city, China. After concentrating and isolating the viruses from the sewage samples, NPEVs were detected and molecular typing was performed. Twenty-one different NPEV serotypes were identified. The most isolated EVs were echovirus 11 (E11), followed by coxsackievirus (CV) B5, E6, and CVB3. EV species B prevailed in sewage samples, but variations in the annual frequency of different serotypes were also observed in different seasons, due to spatial and temporal factors. E11 and E6 were detected continuously before 2017, and the number of isolates was relatively stable during the surveillance period. However, after their explosive growth in 2018 and 2019, their numbers suddenly decreased significantly. CVB3 and CVB5 had alternating trends; CVB5 was most frequently detected in 2013 to 2014 and 2017 to 2018, while CVB3 was most frequently detected in 2015 to 2016 and 2020 to 2021. Phylogenetic analysis showed that at least two different transmission chains of CVB3 and CVB5 were prevalent in Guangzhou City. Our results show that in the absence of a comprehensive and systematic EV-related disease surveillance system in China, environmental surveillance is a powerful and effective tool to strengthen and further investigate the invisible transmission of EVs in the population. IMPORTANCE This study surveilled urban sewage samples from north China for 9 years to monitor enteroviruses. Samples were collected, processed, and viral identification and molecular typing were performed. We detected 21 different non-polio enteroviruses (NPEVs) with yearly variations in prevalence and peak seasons. In addition, this study is very important for understanding the epidemiology of EVs during the COVID-19 pandemic, as the detection frequency and serotypes of EVs in sewage changed considerably around 2020. We believe that our study makes a significant contribution to the literature because our results strongly suggest that environmental surveillance is an exceptionally important tool, which can be employed to detect and monitor organisms of public health concern, which would otherwise be missed and under-reported by case-based surveillance systems alone.

Wastewater Reveals the Spatiotemporal Spread of SARS-CoV-2 in the Canton of Ticino (Switzerland) during the Onset of the COVID-19 Pandemic

Wastewater-based epidemiology (WBE) has emerged as an effective tool for monitoring SARS-CoV-2 dynamics during the COVID-19 pandemic. Here, we add a spatial component to WBE and use it to investigate SARS-CoV-2 spread in the canton of Ticino during the onset of the pandemic in Switzerland (end of February 2020 to beginning of March 2020). Ticino is located at the border to Northern Italy, where a large COVID-19 outbreak occurred in February 2020. Not surprisingly, Ticino was the site of the first clinically confirmed COVID-19 case in Switzerland. We retrospectively analyzed daily influent samples from nine wastewater treatment plants in Ticino that jointly cover an area of 20 km × 60 km and 351,000 people (>99% of the population). Our result is a fine-grained view of the spatiotemporal evolution of the COVID-19 pandemic in this canton. The wastewater analysis revealed that by February 29, 2020, SARS-CoV-2 had already spread to all catchments. At the same time, only four individual cases had been clinically confirmed across the region served by the treatment plants investigated. Our results demonstrate that WBE could serve as a versatile tool to monitor the introduction and spread of an infectious agent on a regional scale. To fully exploit its utility, WBE should be implemented in real time and become an integral part of future disease surveillance efforts.

Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers

COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.

Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers

COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.

Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests

Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per μL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.