Biology subjects

de Korne-Elenbaas, J.

Publications and source records attributed to de Korne-Elenbaas, J..

4 recordsLinked to original sources

bioRxiv2025

Importance of a heat snap in RT-PCR quantification of rotavirus double-stranded RNA in wastewater

Quantification of copies of double stranded RNA using RT-PCR methods may require denaturation of the double stranded structure using an initial high temperature incubation followed by rapid cooling, herein called "heat snap". Papers in the literature that report rotavirus RNA concentrations in fecal and environmental samples do not consistently report the use of such a "heat snap". In this study, we quantified rotavirus RNA in diverse environmental samples (wastewater solids, wastewater, and drainage samples) using digital RT-PCR methods with and without a heatsnap. Concentrations were higher in samples by a factor of 125 when a heat snap was applied. This was consistent across sample types, and across laboratories and PCR instrumentation. We recommend a heat snap be used when enumerating double stranded RNA from rotavirus and other viruses in environmental samples.

molecular biology↗

bioRxiv2025

Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates

Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the gradual degradation of the viral content of the wastewater over time. Testing protocols are complex and often cannot be performed on site, resulting in delays between collection and testing. The evidence of continued degradation of viral RNA when stored at low temperatures is currently limited to a small number of studies with mixed results. Taking advantage of variable delays between sample collection and processing, we used a Bayesian temporal model and data from two winter periods of a national surveillance program in Switzerland to determine the rate at which the measured viral concentrations of four respiratory viruses declined as a result of RNA degradation between sample collection and processing. We found evidence of substantial degradation between the collection and processing of samples with daily rates of up to -0.28 (-0.38 - -0.19 95% CrI). We established that reduction in viral concentrations resulting from post-sampling degradation was responsible for a number of measurements falling below quantifiable limits. For one treatment plant, we estimate that 39 measurements fell below the limit of detection due to RNA degradation over the course of a single season. Measurements are more likely to be lost early in the seasonal epidemic when concentrations are still low. This delays consistent reliable measurement and sets back epidemiological assessments relevant to public health management strategies.

microbiology↗

bioRxiv2020

Emergence of a cephalosporin reduced susceptible Neisseria gonorrhoeae clone between 2014-2019 in Amsterdam, the Netherlands, revealed by a genomic population analysis

BackgroundEmerging resistance to cephalosporins in Neisseria gonorrhoeae (Ng) is a major public health threat, since these are considered antibiotics of last resort. Continuous surveillance is needed to monitor the circulation of reduced susceptible and resistant strains. AimFor the purpose of epidemiological surveillance, a genomic population analysis was performed on Ng isolates from Amsterdam with a focus on ceftriaxone reduced susceptible isolates. MethodsWhole genome sequences were obtained from 318 isolates from 2014-2019 from Amsterdam, the Netherlands. Isolates were typed according to the Multi-Locus Sequence Typing (MLST) scheme and resistance markers were identified. Phylogenetic trees were created to identify genetic clusters and to compare Dutch- and global MLST7827 isolates. ResultsThe majority of ceftriaxone reduced susceptible isolates belonged to MLST7363, MLST1901 and MLST7827. MLST7363 and MLST1901 were dominant reduced susceptible strains from 2014-2016 although MLST7827 emerged and became dominant during 2017-2019. MLST7827 reduced susceptible isolates carried a non-mosaic penA gene with A501V mutation and porB G121K/A121D mutations, which were lacking in susceptible MLST7827 isolates. Phylogenetic analysis of all publicly available MLST7827 isolates showed strong genetic clustering of Dutch- and other European MLST7827 isolates. ConclusionCeftriaxone reduced susceptible MLST7827 isolates emerged during recent years in Amsterdam. Co-occurrence of penA A501V and porB G121K/A121D mutations was strongly associated with ceftriaxone reduced susceptibility. Genetic clustering of Dutch- and other European MLST7827 isolates indicates extensive circulation of this strain in Europe. Therefore, close monitoring of the spread of this strain with an alarming susceptibility profile is needed.

genomics↗

bioRxiv2020

The sudden emergence of a Neisseria gonorrhoeae strain with reduced susceptibility to extended-spectrum cephalosporins, Norway

The Neisseria gonorrhoeae multilocus sequence type (ST) 7827 emerged in dramatic fashion in Norway in the period 2016-2018. Here, we aim to determine what enabled it to establish and spread so quickly. In Norway, ST-7827 isolates were almost exclusively isolated from men. Phylogeographic analyses demonstrated an Asian origin of the ST with multiple importation events to Europe. The ST was uniformly resistant to fluoroquinolones and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESC) cefixime and ceftriaxone. We identified additional independent events of acquisition of penA and porB alleles in Europe, associated with further reduction in cefixime and ceftriaxone susceptibility, respectively. Transmission of the ST was largely curbed in Norway in 2019, but our results indicate the existence of a reservoir in Europe. The worrisome drug resistance profile and rapid emergence of ST-7827 calls for close monitoring of the situation.

genomics↗