The contribution of community and hospital sources to the transmission of extended-spectrum β-lactamase producing Enterobacterales (ESBL-PE) remains elusive. To investigate the extent of community dissemination and the contribution of hospitals to the spread of ESBL-PE by exploring their spatiotemporal distribution in municipal wastewater of the central European city of Basel. Wastewater samples were collected monthly for two consecutive years throughout Basel, Switzerland, including 21 sites across 10 postcode areas of the city collecting either community wastewater (urban sites, n = 17) or community and hospital wastewater (mixed sites, n = 4). Presumptive ESBL-PE were recovered by selective culture methods. Standard methodologies were applied for species identification, ESBL-confirmation, and quantification. Ninety-five percent (477/504) of samples were positive for ESBL-PE. Among these isolates, Escherichia coli (85%, 1,140/1,334) and Klebsiella pneumoniae (11%, 153/1,334) were most common. They were recovered throughout the sampling period from all postcodes, with E. coli consistently predominating. The proportion of K. pneumoniae isolates was higher in wastewater samples from mixed sites as compared to samples from urban sites, while the proportion of E. coli was higher in samples from urban sites (p = 0.003). Higher numbers of colony forming units (CFUs) were recovered from mixed as compared to urban sites (median 3.2 × 102 vs. 1.6 × 102 CFU/mL). E. coli-counts showed moderate correlation with population size (rho = 0.44), while this correlation was weak for other ESBL-PE (rho = 0.21). ESBL-PE are widely spread in municipal wastewater supporting that community sources are important reservoirs entertaining the spread of ESBL-PE. Hospital-influenced abundance of ESBL-PE appears to be species dependent.

AbstractInfluenza infections are challenging to monitor at the population level due to a high proportion of mild and asymptomatic cases and confounding of symptoms with other common circulating respiratory diseases, including COVID-19. Alternate methods capable of tracking cases outside of clinical reporting infrastructure could improve monitoring of influenza transmission dynamics. Influenza shedding into wastewater represents a promising source of information where quantification is unbiased by testing or treatment-seeking behaviors. We quantified influenza A and B virus loads from influent at Switzerland’s three largest wastewater treatment plants, serving about 12% of the Swiss population. We estimated trends in infection incidence and the effective reproductive number Re in these catchments during a 2021/22 epidemic and compared our estimates to clinical influenza surveillance data. We showed that wastewater-based incidence is better aligned with catchment-level confirmed cases than national ILI, and that only the wastewater data capture a peak in incidence in December 2021. We further estimated Re to have been below 1.05 after introduction of work from home measures in December 2021 and above 0.97 after these measures were relaxed in two out of three catchments based on wastewater data. The third catchment yielded qualitatively the same results, although with wider confidence intervals. The confirmed-case data yielded comparatively less precise estimates that include 1 before and during the period of measures. On the basis of this research we developed an online dashboard for wastewater-based influenza surveillance in Switzerland where we will continue to monitor the onset and dynamics of the 2022/23 flu season.

ObjectivesMatrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. MethodsFor baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. ResultsAt baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2–25]), reproducibility between technical replicates (range = [55%–86%]), and measurement error (range = [147 parts per million (ppm)–588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). DiscussionWe have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.

IntroductionWater supply and air-conditioner cooling towers (ACCT) are potential sources of Legionella pneumophila infection in people. During outbreaks, traditional typing methods cannot sufficiently segregate L. pneumophila strains to reliably trace back transmissions to these artificial water systems. Moreover, because multiple L. pneumophila strains may be present within these systems, methods to adequately distinguish strains are needed. Whole genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST), with their higher resolution are helpful in this respect. In summer 2017, the health administration of the city of Basel detected an increase of L. pneumophila infections compared with previous months, signalling an outbreak.AimWe aimed to identify L. pneumophila strains populating suspected environmental sources of the outbreak, and to assess the relations between these strains and clinical outbreak strains.MethodsAn epidemiological and WGS-based microbiological investigation was performed, involving isolates from the local water supply and two ACCTs (n = 60), clinical outbreak and non-outbreak related isolates from 2017 (n = 8) and historic isolates from 2003–2016 (n = 26).ResultsIn both ACCTs, multiple strains were found. Phylogenetic analysis of the ACCT isolates showed a diversity of a few hundred allelic differences in cgMLST. Furthermore, two isolates from one ACCT showed no allelic differences to three clinical isolates from 2017. Five clinical isolates collected in the Basel area in the last decade were also identical in cgMLST to recent isolates from the two ACCTs.ConclusionCurrent outbreak-related and historic isolates were linked to ACCTs, which form a complex environmental habitat where strains are conserved over years.

Abstract. The classical approach of using 137Cs as a soil erosion tracer is based on the comparison between stable reference sites and sites affected by soil redistribution processes; it enables the derivation of soil erosion and deposition rates. The method is associated with potentially large sources of uncertainty with major parts of this uncertainty being associated with the selection of the reference sites. We propose a decision support tool to Check the Suitability of reference Sites (CheSS). Commonly, the variation among 137Cs inventories of spatial replicate reference samples is taken as the sole criterion to decide on the suitability of a reference inventory. Here we propose an extension of this procedure using a repeated sampling approach, in which the reference sites are resampled after a certain time period. Suitable reference sites are expected to present no significant temporal variation in their decay-corrected 137Cs depth profiles. Possible causes of variation are assessed by a decision tree. More specifically, the decision tree tests for (i) uncertainty connected to small-scale variability in 137Cs due to its heterogeneous initial fallout (such as in areas affected by the Chernobyl fallout), (ii) signs of erosion or deposition processes and (iii) artefacts due to the collection, preparation and measurement of the samples; (iv) finally, if none of the above can be assigned, this variation might be attributed to turbation processes (e.g. bioturbation, cryoturbation and mechanical turbation, such as avalanches or rockfalls). CheSS was exemplarily applied in one Swiss alpine valley where the apparent temporal variability called into question the suitability of the selected reference sites. In general we suggest the application of CheSS as a first step towards a comprehensible approach to test for the suitability of reference sites.

Lipsticks and lip care products may contain saturated hydrocarbons which either stem from mineral oil saturated hydrocarbons (MOSH) or are synthetic, that is polyolefin oligomeric saturated hydrocarbons (POSH). Some of these hydrocarbons are strongly accumulated and form granulomas in human tissues, which prompted Cosmetics Europe (former Colipa) to issue a recommendation for their use in lip care and oral products. From 2012 to 2014, MOSH+POSH were determined in 175 cosmetic lip products taken from the Swiss market in order to estimate their contribution to human exposure. Mineral oil saturated hydrocarbons and POSH were extracted and analysed by GC with FID. Areas were integrated as a total as well as by mass ranges with cuts at n-C25 and n-C34 to characterize the molecular mass distribution. About 68% of the products contained at least 5% MOSH+POSH (total concentration). For regular users, these products would be major contributors to their MOSH+POSH exposure. About 31% of the products contained more than 32% MOSH+POSH. Their regular usage would amount in an estimated MOSH+POSH exposure exceeding the highest estimated dietary exposure. The majority of the products contained hydrocarbons with a molecular mass range which was not in line with the recommendations of Cosmetics Europe. Taking into account that material applied to the lips largely ends up being ingested, MOSH and POSH levels should be reduced in the majority of cosmetic lip products. As the extensive evaluation of the data available on MOSH (EFSA J., 10, 2012, 2704) did not enable the specification of limits considered as safe, the present level of dietary exposure and its evaluation as 'of potential concern' provide the relevant bench mark, which means that lip products should contain clearly less than 5% MOSH+POSH.

The optimization and validation of a method for the determination of phosphine in plant materials are described. The method is based on headspace sampling over the sample heated in 5% sulfuric acid. Critical factors such as sample amount, equilibration conditions, method of quantitation, and matrix effects are discussed, and validation data are presented. Grinding of coarse samples does not lead to lower results and is a prerequisite for standard addition experiments, which present the most reliable approach for quantitation because of notable matrix effects. Two interlaboratory comparisons showed that results varied considerably and that an uncertainty of measurement of about 50% has to be assessed. Flame photometric and mass spectrometric detection gave similar results. The proposed method is well reproducible within one laboratory, and results from the authors' laboratories using different injection and detection techniques are very close to each other. The considerable variation in the interlaboratory comparison shows that this analysis is still challenging in practice and further proficiency testing is needed.

The handling of infectious viral vectors such as adenovirus type 5 (Ad5), lentivirus (HIV1), and vaccinia virus (VV) requires biosafety level 2 (BSL-2) containment. This also applies to modified va...

Treatment of dead bacteria with propidium monoazide (PMA) prior to DNA extraction has been described to inhibit subsequent amplification of DNA by polymerase chain reaction (PCR) methods. As an enforcement authority involved in the surveillance of compliance with biosafety regulations, the State Laboratory of Basel City swabs surfaces to check for contaminations with microorganisms. To evaluate the PMA-PCR method for its use in distinguishing DNA from living and dead bacteria in swab samples, we used Staphylococcus aureus as a model organism. In this study PMA treatment was able to reduce amplification of DNA from dead bacteria by a factor of 1,000. However, PMA also entered living S. aureus to some extent, resulting in a reduction of DNA amplification by a factor of 10. When cells were spotted on a dry surface and collected again by wiping, cells were still viable on agar plates, but a distinction between DNA from living or dead bacteria was no longer possible using the PMA-PCR method. The process of drying and wiping seemed to interfere with the membrane of S. aureus resulting in diffusion of PMA into still viable cells. The authors conclude that this method offers a limited capacity to distinguish between living and dead S. aureus in liquid culture but does not allow determining the amount of living S. aureus cells in wipe-samples.