Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study

Abstract Background Cardiovascular disease (CVD) imposes much mortality and morbidity worldwide. The use of “deep learning”, advancements in genomics, metabolomics, proteomics and devices like wearables have the potential to unearth new insights in the field of cardiology. Currently, in Asia, there are no studies that combine the use of conventional clinical information with these advanced technologies. We aim to harness these new technologies to understand the development of cardiovascular disease in Asia. Methods Singapore is a multi-ethnic country in Asia with well-represented diverse ethnicities including Chinese, Malays and Indians. The SingHEART study is the first technology driven multi-ethnic prospective population-based study of healthy Asians. Healthy male and female subjects aged 21–69 years old without any prior cardiovascular disease or diabetes mellitus will be recruited from the general population. All subjects are consented to undergo a detailed on-line questionnaire, basic blood investigations, resting and continuous electrocardiogram and blood pressure monitoring, activity and sleep tracking, calcium score, cardiac magnetic resonance imaging, whole genome sequencing and lipidomic analysis. Outcomes studied will include mortality and cause of mortality, myocardial infarction, stroke, malignancy, heart failure, and the development of co-morbidities. Discussion An initial target of 2500 patients has been set. From October 2015 to May 2017, an initial 683 subjects have been recruited and have completed the initial work-up the SingHEART project is the first contemporary population-based study in Asia that will include whole genome sequencing and deep phenotyping: including advanced imaging and wearable data, to better understand the development of cardiovascular disease across different ethnic groups in Asia.

Download Full-text

Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units

Frontiers in Public Health ◽

10.3389/fpubh.2020.00003 ◽

2020 ◽

Vol 8 ◽

Cited By ~ 4

Author(s):

Bárbara Magalhães ◽

Benoit Valot ◽

Mohamed M. H. Abdelbary ◽

Guy Prod'hom ◽

Gilbert Greub ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Intensive Care ◽

Whole Genome Sequencing ◽

Intensive Care Units ◽

Genome Sequencing ◽

Molecular Typing ◽

Whole Genome

Download Full-text

SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

Clinical Chemistry ◽

10.1093/clinchem/hvaa187 ◽

2020 ◽

Vol 66 (11) ◽

pp. 1450-1458 ◽

Cited By ~ 5

Author(s):

Divinlal Harilal ◽

Sathishkumar Ramaswamy ◽

Tom Loney ◽

Hanan Al Suwaidi ◽

Hamda Khansaheb ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Social Life ◽

Population Based ◽

Viral Transmission ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Genome Amplification ◽

And Control

Abstract Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results We found considerable improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome, compared to an average of 0.63% without enrichment. Consequently, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.

Download Full-text

Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant

Italian Journal of Food Safety ◽

10.4081/ijfs.2017.6879 ◽

2017 ◽

Vol 6 (3) ◽

Cited By ~ 10

Author(s):

Federica Palma ◽

Frédérique Pasquali ◽

Alex Lucchi ◽

Alessandra De Cesare ◽

Gerardo Manfreda

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Typing ◽

Virulence Genes ◽

Processing Plant ◽

Whole Genome ◽

Meat Processing ◽

Typing Methods ◽

Rabbit Meat

Listeria monocytogenes is a food-borne pathogen able to survive and grow in different environments including food processing plants where it can persist for month or years. In the present study the discriminatory power of Whole Genome Sequencing (WGS)-based analysis (cgMLST) was compared to that of molecular typing methods on 34 L. monocytogenes isolates collected over one year in the same rabbit meat processing plant and belonging to three genotypes (ST14, ST121, ST224). Each genotype included isolates indistinguishable by standard molecular typing methods. The virulence potential of all isolates was assessed by Multi Virulence-Locus Sequence Typing (MVLST) and the investigation of a representative database of virulence determinant genes. The whole genome of each isolate was sequenced on a MiSeq platform. The cgMLST, MVLST, and in silico identification of virulence genes were performed using publicly available tools. Draft genomes included a number of contigs ranging from 13 to 28 and N50 ranging from 456298 to 580604. The coverage ranged from 41 to 187X. The cgMLST showed a significantly superior discriminatory power only in comparison to ribotyping, nevertheless it allows the detection of two singletons belonging to ST14 that were not observed by other molecular methods. All ST14 isolates belonged to VT107, which 7-loci concatenated sequence differs for only 4 nucleotides to VT1 (Epidemic clone III). Analysis of virulence genes showed the presence of a fulllength inlA version in all ST14 isolates and of a mutated version including a premature stop codon (PMSC) associated to attenuated virulence in all ST121 isolates.

Download Full-text

Managing incidental findings in population based biobank research

Norsk Epidemiologi ◽

10.5324/nje.v21i2.1494 ◽

2012 ◽

Vol 21 (2) ◽

Cited By ~ 4

Author(s):

Berge Solberg ◽

Kristin Solum Steinsbekk

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Incidental Findings ◽

Basic Research ◽

Population Based ◽

Ethical Framework ◽

Illustrative Case ◽

Whole Genome ◽

Biobank Research ◽

Norwegian Population

With the introduction of whole genome sequencing in medical research, the debate on how to handle incidental findings is becoming omnipresent. Much of the literature on the topic so far, seems to defend the researcher’s duty to inform, the participant’s right to know combined with a thorough informed consent in order to protect and secure high ethical standards in research. In this paper, we argue that this ethical response to incidental findings and whole genome sequencing is appropriate in a clinical context, in what we call therapeutic research. However, we further argue, that it is rather inappropriate in basic research, like the research going on in public health oriented population based biobanks. Our argument is based on two premises: First, in population based biobank research the duties and rights involved are radically different from a clinical based setting. Second, to introduce the ethical framework from the clinical setting into population based basic research, is not only wrong, but it may lead to unethical consequences. A Norwegian population based biobank and the research-ethical debate in Norway on the regulation of whole genome sequencing is used as an illustrative case to demonstrate the pitfalls when approaching the debate on incidental findings in population based biobank research.

Download Full-text

SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

10.1101/2020.06.06.138339 ◽

2020 ◽

Author(s):

Divinlal Harilal ◽

Sathishkumar Ramaswamy ◽

Tom Loney ◽

Hanan Al Suwaidi ◽

Hamda Khansaheb ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Social Life ◽

Population Based ◽

Viral Transmission ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Genome Amplification ◽

And Control

AbstractBackgroundWith the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented.MethodsWe performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences.ResultsWe show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.ConclusionsSARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.

Download Full-text

Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota

10.1101/544502 ◽

2019 ◽

Author(s):

Kaisa Thorell ◽

Linn Inganäs ◽

Annette Backhans ◽

Lars Agréus ◽

Åke Öst ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Amplicon Sequencing ◽

Population Based ◽

Whole Genome ◽

Pathogenic Potential ◽

Human Microbiota ◽

16S Amplicon Sequencing ◽

Increased Risk ◽

Brachyspira Aalborgi

AbstractColonic spirochaetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance and only few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. In these individuals, 17 (2.3 %) had colonic spirochaetosis, which was associated with eosinophilic infiltration and a three-fold increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochaetosis we successfully isolated, cultured and performed whole genome sequencing of in total 17 isolates including theBrachyspira aalborgitype strain 513AT. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and non-spirochaetosis controls.This is the first report of whole genome analysis of clinical isolates from individuals with colonic spirochaetosis. We found one isolate to be of the speciesBrachyspira pilosicoliand all remaining isolates were of the speciesBrachyspira aalborgi. Besides displaying extensive genetic heterogeneity, the isolates harboured several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies fail to detectBrachyspiradue to primer incompatibility. This failure to detect colonic spirochaetosis should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.

Download Full-text