Expanding the Pathogen Panel in Wastewater Epidemiology to Influenza and Norovirus.

Since the start of the 2019 pandemic, wastewater-based epidemiology (WBE) has proven to be a valuable tool for monitoring the prevalence of SARS-CoV-2. With methods and infrastructure being settled, it is time to expand the potential of this tool to a wider range of pathogens. We used over 500 archived RNA extracts from a WBE program for SARS-CoV-2 surveillance to monitor wastewater from 11 treatment plants for the presence of influenza and norovirus twice a week during the winter season of 2021/2022. Extracts were analyzed via digital PCR for influenza A, influenza B, norovirus GI, and norovirus GII. Resulting viral loads were normalized on the basis of NH4-N. Our results show a good applicability of ammonia-normalization to compare different wastewater treatment plants. Extracts originally prepared for SARS-CoV-2 surveillance contained sufficient genomic material to monitor influenza A, norovirus GI, and GII. Viral loads of influenza A and norovirus GII in wastewater correlated with numbers from infected inpatients. Further, SARS-CoV-2 related non-pharmaceutical interventions affected subsequent changes in viral loads of both pathogens. In conclusion, the expansion of existing WBE surveillance programs to include additional pathogens besides SARS-CoV-2 offers a valuable and cost-efficient possibility to gain public health information.

Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale.

SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.

Quest for Optimal Regression Models in SARS-CoV-2 Wastewater Based Epidemiology.

Wastewater-based epidemiology is a recognised source of information for pandemic management. In this study, we investigated the correlation between a SARS-CoV-2 signal derived from wastewater sampling and COVID-19 incidence values monitored by means of individual testing programs. The dataset used in the study is composed of timelines (duration approx. five months) of both signals at four wastewater treatment plants across Austria, two of which drain large communities and the other two drain smaller communities. Eight regression models were investigated to predict the viral incidence under varying data inputs and pre-processing methods. It was found that population-based normalisation and smoothing as a pre-processing of the viral load data significantly influence the fitness of the regression models. Moreover, the time latency lag between the wastewater data and the incidence derived from the testing program was found to vary between 2 and 7 days depending on the time period and site. It was found to be necessary to take such a time lag into account by means of multivariate modelling to boost the performance of the regression. Comparing the models, no outstanding one could be identified as all investigated models are revealing a sufficient correlation for the task. The pre-processing of data and a multivariate model formulation is more important than the model structure.

Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature.

SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at -20 °C led to a significant reduction in gene copy numbers.

The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool.

Most commonly, next generation sequencing-based microbiome studies are performed on the total DNA (totDNA) pool; however, this consists of extracellular- (exDNA) and intracellular (iDNA) DNA fractions. By investigating the microbiomes of different anaerobic digesters over time, we found that totDNA suggested lower species richness considering all and/or only common species and yielded fewer unique reads as compared to iDNA. Additionally, exDNA-derived sequences were more similar to those from totDNA than from iDNA and, finally, iDNA showed the best performance in tracking temporal changes in microbial communities. We postulate that abundant sequences present within the exDNA fraction mask the overall results of totDNA and provide evidence that exDNA has the potential to qualitatively bias microbiome studies at least in the anaerobic digester environment as it contains information about cells that were lysed hours or days ago. iDNA, however, was found to be more appropriate in providing reliable genetic information about potentially alive as well as rare microbes within the target habitat.

Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.

Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.

Month-of-birth-effect in multiple sclerosis in Austria.

BACKGROUND: The month-of-birth-effect (MoBE) describes the finding that multiple sclerosis (MS) patients seem to have been born significantly more frequently in spring, with a rise in May, and significantly less often in autumn and winter with the fewest births in November. OBJECTIVES: To analyse if the MoBE can also be found in the Austrian MS population, and if so, whether the pattern is similar to the reported pattern in Canada, United Kingdom, and some Scandinavian countries. METHODS: The data of 7886 MS patients in Austria were compared to all live births in Austria from 1940 to 2010, that is, 7.256545 data entries of the Austrian birth registry and analysed in detail. RESULTS: Patterns observed in our MS cohort were not different from patterns in the general population, even when stratifying for gender. However, the noticeable and partly significant ups and downs over the examined years did not follow the distinct specific pattern with highest birth rates in spring and lowest birth rates in autumn that has been described previously for countries above the 49th latitude. CONCLUSION: After correcting for month-of-birth patterns in the general Austrian population, there is no evidence for the previously described MoBE in Austrian MS patients.

Thrombolysis and clinical outcome in patients with stroke after implementation of the Tyrol Stroke Pathway: a retrospective observational study.

BACKGROUND: Intravenous thrombolysis for ischaemic stroke remains underused worldwide. We aimed to assess whether our statewide comprehensive stroke management programme would improve thrombolysis use and clinical outcome in patients. METHODS: In 2008-09, we designed the Tyrol Stroke Pathway, which provided information campaigns for the public and standardised the entire treatment pathway from stroke onset to outpatient rehabilitation. It was commenced in Tyrol, Austria, as a long-term routine-care programme and aimed to include all patients with stroke in the survey area. We focused on thrombolysis use and outcome in the first full 4 years of implementation (2010-13). FINDINGS: We enrolled 4947 (99%) of 4992 patients with ischaemic stroke who were admitted to hospitals in Tyrol; 675 (14%) of the enrollees were treated with alteplase. Thrombolysis administration in Tyrol increased after programme implementation, from 160 of 1238 patients (12·9%, 95% CI 11·1-14·9) in 2010 to 213 of 1266 patients (16·8%, 14·8-19·0) in 2013 (ptrend 2010-13<0·0001). Differences in use of thrombolysis in the nine counties of Tyrol in 2010 (range, 2·2-22·6%) were reduced by 2013 (12·1-22·5%). Median statewide door-to-needle time decreased from 49 min (IQR 35-60) in 2010 to 44 min (29-60) in 2013; symptomatic post-thrombolysis intracerebral haemorrhages occurred in 28 of 675 patients (4·1%, 95% CI 2·8-5·9) during 2010-13. In four Austrian states without similar stroke programmes, thrombolysis administration remained stable or declined between 2010 and 2013 (mean reduction 14·4%, 95% CI 10·9-17·9). Although the 3-month mortality was not affected by our programme (137 [13%] of 1060 patients in 2010 vs 143 [13%] of 1069 patients in 2013), 3-month functional outcome significantly improved (modified Rankin Scale score 0-1 in 375 [40%] of 944 patients in 2010 vs 493 [53%] of 939 in 2013; score 0-2 in 531 [56%] patients in 2010 and 615 [65%] in 2013; ptrend 2010-13<0·0001). INTERPRETATION: During the period of implementation of our comprehensive stroke management programme, thrombolysis administration increased and clinical outcome significantly improved, although mortality did not change. We hope that these results will guide health authorities and stroke physicians elsewhere when implementing similar programmes for patients with stroke. FUNDING: Reformpool of the Tyrolean Health Care Fund.

Spontaneous localized intestinal perforation in very-low-birth-weight infants: a distinct clinical entity different from necrotizing enterocolitis.

BACKGROUND: Idiopathic spontaneous intestinal perforation (SIP), a distinct clinical entity different from necrotizing enterocolitis (NEC), has an increasing prevalence in very-low-birth-weight infants. The aims of our study were to define patient characteristics and potential risk factors for premature infants with SIP compared with infants subjected to surgical treatment for NEC. STUDY DESIGN: The medical records of 29 premature infants with either SIP (n = 13) or NEC (n = 16) were reviewed retrospectively. RESULTS: Infants who experienced SIP were smaller at birth, had lower Apgar scores, and required more intensive neonatal resuscitation. An increased rate of premature rupture of membranes in infants with SIP (8/13 versus 6/16) was not associated with a higher rate of infection in mothers or infants. The onset of illness in SIP was significantly earlier than in NEC (p = 0.022). In contrast to patients with NEC (7/16), 11 of 13 patients in the SIP group had received indomethacin (p = 0.02). Bluish discoloration of the abdomen (8/13), a gasless abdomen (8/13), and the absence of pneumatosis intestinalis (0/13) were further significant markers in infants with SIP. At operation, SIP was always located in the terminal ileum in an antimesenteric position (13/13), and the remaining bowel appeared grossly normal. In most cases of SIP (10/13), the histologic investigation revealed an area of hemorrhagic necrosis without the typical coagulation necrosis seen predominantly in NEC. CONCLUSIONS: Based on clinical presentation and radiologic and intraoperative findings, SIP is a distinct pathologic entity in very-low-birth-weight infants and can be differentiated from classic NEC. Detected early, SIP can be treated by simple procedures (sutures, or resection and primary anastomosis) with a low rate of morbidity and mortality.