Revue des principales méthodes d’identification des sources de pollutions fécales des eaux et coquillages

Les contaminations fécales des eaux et des coquillages induisent des risques pour la santé humaine et des pertes économiques liées, entre autres, aux interdictions de baignade et à la fermeture des zones de conchyliculture. La réduction des apports à l’origine de cette contamination est facilitée par une identification précise des sources (humaines ou animales) qui peut aussi servir à hié rarchiser les mesures à adopter en cas de besoin. De nombreux marqueurs ont été proposés à ce titre durant les deux dernières décennies. Ils correspondent :-à des micro-organismes (bactéries, virus ou bactériophages) mis en évidence par des approaches culturales, biochimiques ou moléculaires; -à des molécules chimiques présentes naturellement dans les fèces ou associées à l’une des sources de pollution; -et à la mise en évidence de cellules spécifiques de l’hôte dissimulées dans les matières fécales. Cet article présente ces différentes methods d’identification des sources de contaminations fécales en décrivant leur utilisation et la nature des résultats qu’elles permettent d’obtenir. Le principal corollaire de cette revue bibliographique est qu’il semble nécessaire de coupler différents marqueurs pour pouvoir identifier les sources

Detection of small amounts of human adenoviruses in stools: comparison of a new immuno real-time PCR assay with classical tools

AbstractThe detection of low virus concentrations in biological matrices, especially stool samples, is facing significant limitations as far as common diagnostic methods (enzyme-linked-immunosorbent assay (ELISA) or quantitative real-time PCR (qPCR)) are considered. Here the development of a new immuno real-time PCR (iPCR) is described and its performance in the detection of human adenoviruses (HAdVs) in spiked stools is compared with those of ELISA and qPCR assays. For the iPCR, detection of the sandwich formed by the complexation of capture antibody-antigen-detection antibody was performed by qPCR thanks to the substitution of peroxydase by a chimeric DNA. This modification increased the detection sensitivity 200-fold compared to ELISA. The direct qPCR results revealed that only 0.3–9.5% of the spiked HAdV were detectable, resulting from important losses of DNA occurring at the extraction step. This step was not necessary in the iPCR workflow, avoiding this drawback. The losses of viral particles occurred at the elution step from the stool only. The recovery rate of the iPCR was thus better and ranged between 21 and 54%. As a result, iPCR enabled the detection of lower virus concentrations in stool samples compared to those detected by ELISA and qPCR. The iPCR could be considered as a ‘hyper sensitive ELISA’ for early detection of HAdV infections, especially in the case of immunocompromised patients after haematopoietic stem cell transplant

Making waves: collaboration in the time of SARS-CoV-2 - rapid development of an international co-operation and wastewater surveillance database to support public health decision-making

The presence of SARS-CoV-2 RNA in wastewater was first reported in March 2020. Over the subsequent months, the potential for wastewater surveillance to contribute to COVID-19 mitigation programmes has been the focus of intense national and international research activities, gaining the attention of policy makers and the public. As a new application of an established methodology, focused collaboration between public health practitioners and wastewater researchers is essential to developing a common understanding on how, when and where the outputs of this non-invasive community-level approach can deliver actionable outcomes for public health authorities. Within this context, the NORMAN SCORE "SARS-CoV-2 in sewage" database provides a platform for rapid, open access data sharing, validated by the uploading of 276 data sets from nine countries to-date. Through offering direct access to underpinning meta-data sets (and describing its use in data interpretation), the NORMAN SCORE database is a resource for the development of recommendations on minimum data requirements for wastewater pathogen surveillance. It is also a tool to engage public health practitioners in discussions on use of the approach, providing an opportunity to build mutual understanding of the demand and supply for data and facilitate the translation of this promising research application into public health practice. [Abstract copyright: Copyright © 2021 Elsevier Ltd. All rights reserved.

Rapid and Sensitive Detection of Yersinia pestis Using Amplification of Plague Diagnostic Bacteriophages Monitored by Real-Time PCR

BACKGROUND: Yersinia pestis, the agent of plague, has caused many millions of human deaths and still poses a serious threat to global public health. Timely and reliable detection of such a dangerous pathogen is of critical importance. Lysis by specific bacteriophages remains an essential method of Y. pestis detection and plague diagnostics. METHODOLOGY/PRINCIPAL FINDINGS: The objective of this work was to develop an alternative to conventional phage lysis tests--a rapid and highly sensitive method of indirect detection of live Y. pestis cells based on quantitative real-time PCR (qPCR) monitoring of amplification of reporter Y. pestis-specific bacteriophages. Plague diagnostic phages phiA1122 and L-413C were shown to be highly effective diagnostic tools for the detection and identification of Y. pestis by using qPCR with primers specific for phage DNA. The template DNA extraction step that usually precedes qPCR was omitted. phiA1122-specific qPCR enabled the detection of an initial bacterial concentration of 10(3) CFU/ml (equivalent to as few as one Y. pestis cell per 1-microl sample) in four hours. L-413C-mediated detection of Y. pestis was less sensitive (up to 100 bacteria per sample) but more specific, and thus we propose parallel qPCR for the two phages as a rapid and reliable method of Y. pestis identification. Importantly, phiA1122 propagated in simulated clinical blood specimens containing EDTA and its titer rise was detected by both a standard plating test and qPCR. CONCLUSIONS/SIGNIFICANCE: Thus, we developed a novel assay for detection and identification of Y. pestis using amplification of specific phages monitored by qPCR. The method is simple, rapid, highly sensitive, and specific and allows the detection of only live bacteria

Virus occurrence in private and public wells in a fractured dolostone aquifer in Canada

Groundwater samples from 22 wells completed in a regional fractured dolostone aquifer in the Guelph region of southern Ontario, Canada, were collected over an 8-month period and analyzed for viruses and Campylobacter jejuni. Only 8% of the 118 samples exhibited viruses at extremely low concentrations, but of the 22 wells sampled, 10 (45%) were positive for human enteric viruses (polyomavirus, adenovirus A, and GII norovirus) including 5 of the 8 public supply wells (62.5%) and 5 of the 11 private wells (45%). Each virus-positive well had only one virus occurrence with six sampling events during the 8-month sampling campaign and only one virus type was detected in each well. The probability of virus detection was positively associated with well open-interval length. Virus concentration (in the wells that were virus-positive) was negatively associated with well depth and open-interval length and positively associated with overburden thickness (ie, the thickness of unconsolidated materials overlying bedrock facies) and the amount of precipitation 8–14 and 15–21 days prior to the sampling date. The ephemeral nature of the virus detections and the low detection rate on a per sample basis were consistent with previous studies. The percentage of virus-positive wells, however, was much higher than previous studies, but consistent with the fact that the hydrogeologic conditions of fractured bedrock aquifers create wide capture zones and short groundwater travel times to wells making them more vulnerable to contamination occurrence but at very low concentrations