Metagenomic analysis of viruses in toilet waste from long distance flights—A new procedure for global infectious disease surveillance

Hjelmsø, Mathis Hjort; Mollerup, Sarah; Jensen, Randi Holm; Pietroni, Carlotta; Lukjancenko, Oksana; Schultz, Anna Charlotte; Aarestrup, Frank Møller; Hansen, Anders J.

doi:10.1371/journal.pone.0210368

Cited by 31 publications

(34 citation statements)

References 59 publications

(66 reference statements)

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“…However, such studies have only focused on a single or a limited number of the possible pathogens found in sewage. Despite metagenomics being in its infancy, several recent studies have shown the feasibility of this methodology to identify and quantify a wide range of bacteria, viruses, and antimicrobial resistance (AMR) genes from complex samples such as sewage and wastewater [5,[7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

et al. 2019

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BackgroundWorldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.MethodWe conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.ResultsA large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.ConclusionThe metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.

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Section: Introductionmentioning

confidence: 99%

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

et al. 2019

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“…In fact, with the real picture of the virome in mind, vertebrate viruses are commonly found in low proportions with respect to other viruses such as bacteriophages and plant viruses, which have been described as the most abundant in sewage samples [65,88]. TES has been successfully employed in previous studies [21,49,50,67,68] to improve the detection of vertebrate viruses of interest that would otherwise be difficult due to their low concentrations in environmental samples. Recently, the VirCapSeqVERT Capture Panel was applied in a metagenomic study to evaluate NoV genomic diversity in oysters [50], but to date, no studies have applied this capture approach to fresh fruits and vegetables.…”

Section: Discussionmentioning

confidence: 99%

“…Libraries were equimolarly pooled and captured using the VirCapSeqVERT Capture Panel (Roche, Basel, Switzerland). This panel involves the hybridization of probes designed to capture sequences from vertebrate viral pathogens, and it has enabled the detection of viral sequences in complex sample types in previous studies [21,49,50,67,68]. After the capture, quality and concentration were checked, and captured libraries were sequenced using an Illumina MiSeq 2 × 300 bp platform.…”

Section: Capture Of Viral Sequences By Vircapseq-vert Capture Panelmentioning

confidence: 99%

NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water

Itarte

Martínez-Puchol

Forés

et al. 2021

Foods

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Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.

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“…Areas encompassed by computational biology depend on the specific goals and the types of experimental data that are available, including sequence and structural analysis [60,61] and their correlation with function [62], evolution and population genomics, regulatory [63] and metabolic networks [64], image analysis [65], and disease [66]. Computational biology often addresses tasks by analyzing large genomic [67,68,69,70,71], proteomic, microarray, cell and tissue imaging, and clinical data [72,73] to produce robust statistical trends and correlate these with outcomes. It harnesses high-throughput genomic and proteomic methods to integrate data [74], to identify and validate biomarkers and novel therapeutic targets, and to rapidly translate the findings to the clinic.…”

Section: The Breadth Of Computational Biologymentioning

confidence: 99%

Computational Structural Biology: Successes, Future Directions, and Challenges

et al. 2019

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Computational biology has made powerful advances. Among these, trends in human health have been uncovered through heterogeneous ‘big data’ integration, and disease-associated genes were identified and classified. Along a different front, the dynamic organization of chromatin is being elucidated to gain insight into the fundamental question of genome regulation. Powerful conformational sampling methods have also been developed to yield a detailed molecular view of cellular processes. when combining these methods with the advancements in the modeling of supramolecular assemblies, including those at the membrane, we are finally able to get a glimpse into how cells’ actions are regulated. Perhaps most intriguingly, a major thrust is on to decipher the mystery of how the brain is coded. Here, we aim to provide a broad, yet concise, sketch of modern aspects of computational biology, with a special focus on computational structural biology. We attempt to forecast the areas that computational structural biology will embrace in the future and the challenges that it may face. We skirt details, highlight successes, note failures, and map directions.

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Metagenomic analysis of viruses in toilet waste from long distance flights—A new procedure for global infectious disease surveillance

Cited by 31 publications

References 59 publications

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water

Computational Structural Biology: Successes, Future Directions, and Challenges

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