Preliminary evaluation of BioFire FilmArray® Gastrointestinal Panel for the detection of noroviruses and other enteric viruses from wastewater and shellfish

A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques

Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.

Molecular and Genetics-Based Systems for Tracing the Evolution and Exploring the Mechanisms of Human Norovirus Infections

Human noroviruses (HuNoV) are major causes of acute gastroenteritis around the world. The high mutation rate and recombination potential of noroviruses are significant challenges in studying the genetic diversity and evolution pattern of novel strains. In this review, we describe recent advances in the development of technologies for not only the detection but also the analysis of complete genome sequences of noroviruses and the future prospects of detection methods for tracing the evolution and genetic diversity of human noroviruses. The mechanisms of HuNoV infection and the development of antiviral drugs have been hampered by failure to develop the infectious virus in a cell model. However, recent studies have demonstrated the potential of reverse genetics for the recovery and generation of infectious viral particles, suggesting the utility of this genetics-based system as an alternative for studying the mechanisms of viral infection, such as cell entry and replication.

Detection of Zoonotic Gastrointestinal Pathogens in Dairy Sheep and Goats by Using FilmArray® Multiplex-PCR Technology

The objectives of this study were (a) to detect gastrointestinal pathogens in faecal samples of sheep and goats using the FilmArray® GI Panel and (b) to evaluate factors that were associated with their presence. Faecal samples from ewes or does in 70 sheep flocks and 24 goat herds in Greece were tested for the presence of 22 gastrointestinal pathogens by means of the BioFire® FilmArray® Gastrointestinal (GI) Panel. The most frequently detected pathogens were Shiga-like toxin-producing Escherichia coli stx1/stx2 (94.7% of farms), Giardia lamblia (59.6%), and Campylobacter spp. (50.0% of farms). Other pathogens detected were Cryptosporidium spp., Salmonella spp., enterotoxigenic E. coli lt/st, Yersinia enterocolitica, E. coli O157, Rotavirus A, Shigella/enteroinvasive E. coli, and Plesiomonasshigelloides. There was a difference in the prevalence of detection of pathogens between sheep and goat farms only for Salmonella spp.: 18.3% versus 0.0%, respectively. Mixed infections were detected in 76 farms (80.9% of farms), specifically 57 sheep flocks and 19 goat herds, with on average, 2.5 ± 0.1 pathogens detected per farm. The body condition score of ewes in farms, in which only one pathogen was detected in faecal samples, was significantly higher than that of ewes in farms, in which at least two pathogens were detected: 2.55 ± 0.11 versus 2.31 ± 0.04. In sheep flocks, the number of pathogens in faecal samples was significantly higher in farms with semi-extensive management. In goat herds, the number of pathogens in faecal samples was positively correlated with average precipitation and inversely correlated with temperature range in the respective locations.

Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems

Viruses are omnipresent and persistent in wastewater, which poses a risk to human health. In this review, we summarise the different qualitative and quantitative methods for virus analysis in wastewater and systematically discuss the spatial distribution and temporal patterns of various viruses (i.e., enteric viruses, Caliciviridae (Noroviruses (NoVs)), Picornaviridae (Enteroviruses (EVs)), Hepatitis A virus (HAV)), and Adenoviridae (Adenoviruses (AdVs))) in wastewater systems. Then we critically review recent SARS-CoV-2 studies to understand the ongoing COVID-19 pandemic through wastewater surveillance. SARS-CoV-2 genetic material has been detected in wastewater from France, the Netherlands, Australia, Italy, Japan, Spain, Turkey, India, Pakistan, China, and the USA. We then discuss the utility of wastewater-based epidemiology (WBE) to estimate the occurrence, distribution, and genetic diversity of these viruses and generate human health risk assessment. Finally, we not only promote the prevention of viral infectious disease transmission through wastewater but also highlight the potential use of WBE as an early warning system for public health assessment.

Molecular Monitoring of Enteropathogens in Sewage During NATO Exercise Trident Juncture 2018: Potential Tool in Early Outbreak Warning?

INTRODUCTION

Outbreaks of gastrointestinal disease among military service personnel can have severe impact on operational effectivity and force readiness. Thus, early outbreak detection is critical to minimize spread. This pilot study aimed to explore field-based molecular screening of sewage as a supplemental tool in early outbreak warning before disease is diagnosed in personnel seeking medical care.

MATERIALS AND METHODS

Sewage from permanent (n = 3) and temporary (n = 3) military camps, hosting national and international military personnel, were sampled during the NATO Exercise TRJE18 taking place in southern Norway during fall 2018. Samples were screened for 22 gastrointestinal pathogens using multiplex PCR.

RESULTS

Markers of multiple enteropathogens were detected in samples from all locations with some variations in diversity. Yersinia enterocolitica, pathogenic Escherichia coli, adenovirus, and Giardia were detected in sewage from all six camps during the exercise. Agent diversity seemed to increase with population size, regardless of nationality. Only a minor outbreak (n = 6) of norovirus was reported in one of the permanent camps. From the same camp, genetic markers of norovirus were detected in sewage 2 days before outbreak notification. No other outbreaks of gastrointestinal disease were reported during the exercise, indicating that markers of several enteropathogens can be normally found in sewage from healthy soldier populations. Thus, discriminating between true outbreaks and nonrelevant "background levels" would be of critical importance for correct decision-making in operational contexts.

CONCLUSIONS

Molecular screening of sewage allows rapid detection of multiple gastrointestinal pathogens in biological waste from military camps. However, background levels of pathogens challenges interpretation of qualitative analyses in outbreak situations. As such, quantitative measures, as well as high-resolution sequence-based methods, which allows strain identification and broader target spectrum, should be further explored in future studies.

Diagnostic syndromic multiplex approaches for gastrointestinal infections

Introduction: Gastrointestinal diseases due to infectious pathogens currently represent an important global health concern, especially in children and developing countries. Early and accurate detection of gastrointestinal pathogens is important to initiate the appropriate type of therapy. Multiplex molecular gastrointestinal panels rapidly detect several gastrointestinal pathogens at once with high sensitivity.Areas covered: We assess the scope and limitations of several multiplex gastrointestinal panels approved by the Food and Drug Administration or marked by Conformité Européenne-in vitro diagnostic. We compare 10 syndromic gastrointestinal panels, 14 bacteria-specific multiplex panels, seven parasite-specific multiplex panels, and eight virus-specific multiplex panels.Expert opinion: Thanks to the advances made in the diagnostic approaches for gastrointestinal infections, there are various panels to choose. The choice of a specific syndromic gastrointestinal multiplex panel should be made to improve patient care. Diagnostic syndromic multiplex approaches for gastrointestinal infections should be customized; each hospital should develop its diagnostic algorithm for gastrointestinal infections tailored to its setting, study population, and geographical site. Current multiplex gastrointestinal panels could be improved by including the detection of antimicrobial resistance, toxigenic Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus responsible for the COVID-19 pandemic).

Astrovirus evolution and emergence

Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.

Multiplex polymerase chain reaction detection of enteropathogens in sewage in Norway

The primary objective of this small-scale study was to investigate the occurrence of enteropathogens in sewage (municipal wastewater) in Norway using the commercially available FilmArray^® multiplex polymerase chain reaction (PCR) system with the gastrointestinal (GI) panel. Our findings indicate that DNA/RNA of several enteropathogens are present simultaneously in Norwegian wastewater systems. The spectre was broad even in smaller communities. With some exceptions, occurrence corresponded more or less to the reported cases of infectious human gastrointestinal disease in the same geographical regions. The effects of different sewage purification techniques were assessed on a limited number of samples indicating that neither chemical nor biological treatment was sufficiently effective to reduce gene material from the pathogens to undetectable levels. Further studies are required to assess the performance and suitability FilmArray^® multiplex PCR when used on collective sewage samples in outbreak situations. Additionally, screening sewage samples using multiplex-PCR could be valuable in order to detect new and emerging pathogens and for preliminary analysis of samples before proceeding to more work demanding confirmatory techniques.