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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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Ehman M, Punian J, Weymann D, Regier DA. Next-generation sequencing in oncology: challenges in economic evaluations. Expert Rev Pharmacoecon Outcomes Res 2024:1-18. [PMID: 39096135 DOI: 10.1080/14737167.2024.2388814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 08/04/2024]
Abstract
INTRODUCTION Next-generation sequencing (NGS) identifies genetic variants to inform personalized treatment plans. Insufficient evidence of cost-effectiveness impedes the integration of NGS into routine cancer care. The complexity of personalized treatment challenges conventional economic evaluation. Clearly delineating challenges informs future cost-effectiveness analyses to better value and contextualize health, preference-, and equity-based outcomes. AREAS COVERED We conducted a scoping review to characterize the applied methods and outcomes of economic evaluations of NGS in oncology and identify existing challenges. We included 27 articles published since 2016 from a search of PubMed, Embase, and Web of Science. Identified challenges included defining the evaluative scope, managing evidentiary limitations including lack of causal evidence, incorporating preference-based utility, and assessing distributional and equity-based impacts. These challenges reflect the difficulty of generating high-quality clinical effectiveness and real-world evidence (RWE) for NGS-guided interventions. EXPERT OPINION Adapting methodological approaches and developing life-cycle health technology assessment (HTA) guidance using RWE is crucial for implementing NGS in oncology. Healthcare systems, decision-makers, and HTA organizations are facing a pivotal opportunity to adapt to an evolving clinical paradigm and create innovative regulatory and reimbursement processes that will enable more sustainable, equitable, and patient-oriented healthcare.
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Affiliation(s)
- Morgan Ehman
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Jesman Punian
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Deirdre Weymann
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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Yin L, Pettengill JB. Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases. BMC Res Notes 2024; 17:191. [PMID: 38982485 PMCID: PMC11232179 DOI: 10.1186/s13104-024-06847-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
OBJECTIVES Much has been written about the utility of genomic databases to public health. Within food safety these databases contain data from two types of isolates-those from patients (i.e., clinical) and those from non-clinical sources (e.g., a food manufacturing environment). A genetic match between isolates from these sources represents a signal of interest. We investigate the match rate within three large genomic databases (Listeria monocytogenes, Escherichia coli, and Salmonella) and the smaller Cronobacter database; the databases are part of the Pathogen Detection project at NCBI (National Center for Biotechnology Information). RESULTS Currently, the match rate of clinical isolates to non-clinical isolates is 33% for L. monocytogenes, 46% for Salmonella, and 7% for E. coli. These match rates are associated with several database features including the diversity of the organism, the database size, and the proportion of non-clinical BioSamples. Modeling match rate via logistic regression showed relatively good performance. Our prediction model illustrates the importance of populating databases with non-clinical isolates to better identify a match for clinical samples. Such information should help public health officials prioritize surveillance strategies and show the critical need to populate fledgling databases (e.g., Cronobacter sakazakii).
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Affiliation(s)
- Lanlan Yin
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MA, USA
| | - James B Pettengill
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MA, USA.
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Main DC, Taft JM, Geneva AJ, Jansenvan Vuuren B, Tolley KA. The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons. PeerJ 2024; 12:e17076. [PMID: 38708350 PMCID: PMC11067893 DOI: 10.7717/peerj.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 05/07/2024] Open
Abstract
Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
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Affiliation(s)
- Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Jody M. Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Anthony J. Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Bettine Jansenvan Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
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Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AH, Phillippy AM. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585294. [PMID: 38529488 PMCID: PMC10962732 DOI: 10.1101/2024.03.15.585294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the ultra-long reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes.
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Affiliation(s)
- Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhigui Bao
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, BadenWürttemberg, Germany
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Human Technopole, Milan, Italy
| | - Shujun Ou
- Ohio State University, Columbus, OH, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Katharine M. Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Julian Lucas
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brandy McNulty
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jimin Park
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | | | - Ilse Vrijenhoek
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Adam M. Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (BETHESDA, MD.) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
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Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
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Bonsa Z, Tadesse M, Balay G, Kebede W, Abebe G. Discordance between genotypic and phenotypic methods for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis and the correlation with patient treatment outcomes. J Clin Tuberc Other Mycobact Dis 2024; 34:100410. [PMID: 38225941 PMCID: PMC10788488 DOI: 10.1016/j.jctube.2023.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Background Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB) is essential for proper patient management. We investigated discordance between genotypic (Xpert MTB/RIF and MTBDRplus) and phenotypic (MGIT 960) methods for the detection of rifampicin (RIF) and isoniazid (INH) resistant MTB and its correlation with patient treatment outcomes in Jimma, Southwest Oromia, Ethiopia. Methods A retrospective study was conducted on 57 stored MTB isolates with known Xpert RIF resistance status (45 RIF resistant and 12 RIF susceptible) at Jimma University Mycobacteriology Research Center from November 2, 2021, to December 28, 2022. We did MTBDRplus and phenotypic DST (using the Mycobacterial Growth Indicator Tube (MGIT) system). The Xpert and MTBDRplus results were compared using phenotypic DST as a reference standard method. The treatment outcome was determined as per national guideline. The discordance between the genotypic and phenotypic DST was calculated using GraphPad software. Results Among the 57 MTB isolates, six (10.5 %) had discordant results between the two DST methods. Xpert yielded five discordant results for RIF when compared with phenotypic DST (kappa coefficient (κ) = 0.76, 95 % confidence interval 0.56-0.96). The MTBDRplus compared with phenotypic DST gave three discordant results for RIF (κ = 0.86, 95 % confidence interval 0.71-1.00) and three for INH (κ = 0.86, 95 % confidence interval 0.70-1.00). Compared with Xpert, MTBDRplus yielded lower discordance with phenotypic DST for RIF. Out of six patients with discordant results, three had unfavorable outcomes while the other three were cured. Of the three patients with unfavorable outcomes, only one patient has received an inappropriate treatment regimen. There was no correlation between unfavorable outcomes and incorrect treatment regimens due to discordant results (Χ2 = 0.404; P = 0.525). Conclusions Discordance between genotypic and phenotypic DST for RIF or INH occurred in 10.5 % of isolates. Only one patient with discordant results has received an inappropriate treatment regimen, resulting in an unfavorable outcome. The impact of parallel use of rapid molecular assay with phenotypic DST on patient treatment outcomes requires further study.
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Affiliation(s)
- Zegeye Bonsa
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
| | - Mulualem Tadesse
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
| | - Getu Balay
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
| | - Wakjira Kebede
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
| | - Gemeda Abebe
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
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Hamilton DG, Page MJ, Everitt S, Fraser H, Fidler F. Cancer researchers' experiences with and perceptions of research data sharing: Results of a cross-sectional survey. Account Res 2024:1-28. [PMID: 38299475 DOI: 10.1080/08989621.2024.2308606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Despite wide recognition of the benefits of sharing research data, public availability rates have not increased substantially in oncology or medicine more broadly over the last decade. METHODS We surveyed 285 cancer researchers to determine their prior experience with sharing data and views on known drivers and inhibitors. RESULTS We found that 45% of respondents had shared some data from their most recent empirical publication, with respondents who typically studied non-human research participants, or routinely worked with human genomic data, more likely to share than those who did not. A third of respondents added that they had previously shared data privately, with 74% indicating that doing so had also led to authorship opportunities or future collaborations for them. Journal and funder policies were reported to be the biggest general drivers toward sharing, whereas commercial interests, agreements with industrial sponsors and institutional policies were the biggest prohibitors. We show that researchers' decisions about whether to share data are also likely to be influenced by participants' desires. CONCLUSIONS Our survey suggests that increased promotion and support by research institutions, alongside greater championing of data sharing by journals and funders, may motivate more researchers in oncology to share their data.
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Affiliation(s)
- Daniel G Hamilton
- MetaMelb Research Group, School of BioSciences, University of Melbourne, Melbourne, Australia
- Melbourne Medical School, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Melbourne, Australia
| | - Matthew J Page
- Methods in Evidence Synthesis Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Australia
| | - Sarah Everitt
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Hannah Fraser
- MetaMelb Research Group, School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Fiona Fidler
- MetaMelb Research Group, School of BioSciences, University of Melbourne, Melbourne, Australia
- School of History & Philosophy of Sciences, University of Melbourne, Melbourne, Australia
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Grobe B, Wellhöner F, Klein F, Chhatwal P, Vital M, Pieper DH, Voigtländer T, Lenzen H, Wedemeyer H, Solbach P, Heidrich B. Next Generation Sequencing Outperforms Cultivation-Based Methods for Detection of Bacterial Genera in Bile After Liver Transplantation. J Clin Exp Hepatol 2024; 14:101265. [PMID: 38076367 PMCID: PMC10709207 DOI: 10.1016/j.jceh.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/02/2023] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND AND AIMS Bacterial cholangitis is a common complication in patients with ischemic type biliary lesions and/or anastomotic strictures after liver transplantation (LTX). Patients frequently need antibiotics and endoscopic retrograde cholangiography (ERC) to improve the bile flow. Antibiotic treatment is based on findings in standard microbiological cultivation (SMC) of bile. However, the cultivation techniques are limited to a subset of bacteria easy-to-cultivate. Therefore, the aim of our study was to evaluate the value of next generation sequencing as an additional diagnostic tool to SMC in ischemic type biliary lesions and/or anastomotic strictures. METHODS We sequenced the V1-V2 region of the 16S rRNA gene in 242 stored bile samples in patients after LTX and compared the results with findings of SMC. SMC was performed in n = 135 (56%) fresh bile samples in addition to NGS. SMC was part of the clinical routine in these patients. RESULTS NGS detected bacterial genera in bile samples more often than SMC (P = 5.42 × 10-74). SMC showed insufficient discovery of bacterial genera compared to NGS with better performance in patients receiving antibiotics prior to ERC. SMC missed many bacterial genera detected by NGS. CONCLUSIONS NGS was more sensitive in detecting bacteria in bile than SMC, no clinical parameters could be used to improve discovery rates in SMC and many genera were missed by SMC. Therefore, NGS should be used in a combined approach with SMC for improved diagnostics to achieve more specific and targeted antibiotic treatments.
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Affiliation(s)
- Björn Grobe
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
| | - Freya Wellhöner
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Friederike Klein
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Patrick Chhatwal
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Torsten Voigtländer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Henrike Lenzen
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx), Hannover Medical School, Hannover, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Philipp Solbach
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx), Hannover Medical School, Hannover, Germany
- Medical Department I, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Benjamin Heidrich
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, Hannover 30625, Germany
- Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research, Braunschweig, Germany
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx), Hannover Medical School, Hannover, Germany
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Valiati VH, Lopes F. Editorial: Molecular systematics and phylogeography of tropical and subtropical biodiversity. Front Genet 2023; 14:1345239. [PMID: 38162676 PMCID: PMC10756672 DOI: 10.3389/fgene.2023.1345239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
- Victor Hugo Valiati
- Laboratório de Genética e Biologia Molecular, Programa de Pós-Graduação em Biologia, Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Fernando Lopes
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Stipinovich AM, Tönsing K, Dada S. Communication strategies to support decision-making by persons with aphasia: A scoping review. INTERNATIONAL JOURNAL OF LANGUAGE & COMMUNICATION DISORDERS 2023; 58:1955-1976. [PMID: 37408384 DOI: 10.1111/1460-6984.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND An individual's ability to make autonomous decisions is fundamental to self-determination. The presence of neurological pathology, for example, aphasia, and its associated difficulties with language and/or cognition, may affect an individual's capacity to make decisions, or their ability to reveal their capacity to make decisions. Decision-making by persons with aphasia (PWA) can be enhanced when communication partners are trained and if communication supports are provided, for example, supports that reduce the linguistic and cognitive demands of the task, and/or that facilitate expression. AIMS The main aim of this review is to identify the types of decisions for which persons with post-stroke aphasia receive support, the communication partners involved in supporting decision-making by PWA and the communication strategies implemented to support decision-making by PWA. METHODS & PROCEDURES A multifaceted search strategy was used. Specific keywords were used to search seven electronic databases. Hand-searches of two journals, as well as ancestral searches of the reference lists of selected articles was also performed. Through the application of predefined selection criteria, 16 journal articles, spanning from 1998 to 2021, were selected from the initial yield of 955 articles for inclusion in this review. Data pertaining to the aims of the study were extracted using a data-extraction form. OUTCOMES & RESULTS This review shows that most of the research to date has focused on supporting persons with post-stroke aphasia in decisions pertaining to discharge planning or accommodation, and decisions pertaining to informed consent for participation in research. The communication partners cited most frequently as supporting decision-making by PWA are speech-language pathologists and family members. A range of communication strategies, most of which are components of Supported Conversation Techniques for Adults with Aphasia (SCA™), support decision-making by PWA. The most frequently listed strategies include augmenting information with different modalities, acknowledging the competence of the PWA, thereby inviting initiation and collaboration by the PWA, and the allocation of sufficient time for the decision-making process. CONCLUSIONS & IMPLICATIONS This review presents research trends regarding the support of PWA in decision-making. Future research should focus on the effectiveness of the different strategies identified, and on the support of PWA in the making of a greater variety of complex decisions. WHAT THIS PAPER ADDS What is already known on the subject PWA have the right to be given the opportunity to participate in personally relevant decision-making through all stages of life. Research has shown that decision-making can be enhanced with trained communication partners and if supports are provided that reduce the linguistic and cognitive demands of the task, and that support the expressive abilities of PWA. What this study adds to existing knowledge This scoping review is the first to synthesize the findings of research regarding the types of decisions for which persons with post-stroke aphasia receive support, the communication partners supporting PWA in making these decisions and the communication strategies implemented to support decision-making by PWA. What are the potential or actual clinical implications of this work? Clinicians working with PWA may be sensitized to the role they can play in supporting decision-making by PWA, the current state of the literature regarding types of decisions that may need to be supported, communication partners who can provide such support and communication strategies that may be helpful in this regard.
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Affiliation(s)
- Alexandra M Stipinovich
- Centre for Augmentative and Alternative Communication, University of Pretoria, Pretoria, South Africa
| | - Kerstin Tönsing
- Centre for Augmentative and Alternative Communication, University of Pretoria, Pretoria, South Africa
| | - Shakila Dada
- Centre for Augmentative and Alternative Communication, University of Pretoria, Pretoria, South Africa
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Viver T, López-Causapé C, Ribot-Fraile P, Pérez-Mazón C, López-Solé D, Jiménez-Guerra G, Taltavull B, López-López A. The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot. Sci Rep 2023; 13:18053. [PMID: 37872265 PMCID: PMC10593736 DOI: 10.1038/s41598-023-44668-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
The public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequencing in resource-limited hospitals, other PCR-based strategies could be applied to efficiently monitor the circulating variants without the need to greatly expand the sequencing capacity. In our case, overpassing the technical limitations inherent to a second level hospital, we were able to characterize the weekly distribution of SARS-CoV-2 by the RT-qPCR amplification patterns visualization, single nucleotide polymorphism genotyping, and sequencing of randomly selected samples. All these molecular approaches allowed us to trace the epidemiology of SARS-CoV-2 viruses circulating in Ibiza and Formentera (Balearic Islands, Spain) during the third to the sixth pandemic waves (January 2021-July 2022), in which three major lineages that were considered as VOCs (Alpha, Delta, and Omicron), and many other non-VOC variants were detected and tracked.
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Affiliation(s)
- T Viver
- Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA-CSIC-UIB), Esporles, Spain
| | - C López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Majorca, Illes Balears, Spain
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - P Ribot-Fraile
- Servicio de Microbiología, Hospital Universitario Son Espases, Majorca, Illes Balears, Spain
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - C Pérez-Mazón
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - D López-Solé
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - G Jiménez-Guerra
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - B Taltavull
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - A López-López
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain.
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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Sharaf A, Ndiribe CC, Omotoriogun TC, Abueg L, Badaoui B, Badiane Markey FJ, Beedessee G, Diouf D, Duru VC, Ebuzome C, Eziuzor SC, Jaufeerally Fakim Y, Formenti G, Ghanmi N, Guerfali FZ, Houaga I, Ideozu JE, Katee SM, Khayi S, Kuja JO, Kwon-Ndung EH, Marks RA, Moila AM, Mungloo-Dilmohamud Z, Muzemil S, Nigussie H, Osuji JO, Ras V, Tchiechoua YH, Zoclanclounon YAB, Tolley KA, Ziyomo C, Mapholi N, Muigai AWT, Djikeng A, Ebenezer TE. Bridging the gap in African biodiversity genomics and bioinformatics. Nat Biotechnol 2023; 41:1348-1354. [PMID: 37699986 DOI: 10.1038/s41587-023-01933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Affiliation(s)
- Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Charlotte C Ndiribe
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Taiwo Crossby Omotoriogun
- Biotechnology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
- A.P. Leventis Ornithological Research Institute, University of Jos, Jos, Nigeria
| | - Linelle Abueg
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Bouabid Badaoui
- Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laâyoune, Morocco
| | | | - Girish Beedessee
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Vincent C Duru
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | | | - Samuel C Eziuzor
- Department of Isotope Biogeochemistry, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Nidhal Ghanmi
- Bioinformatics Lab, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Fatma Zahra Guerfali
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis, Tunisia
- University of Tunis El Manar, University Campus Farhat Hached, Tunis, Tunisia
| | - Isidore Houaga
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Josiah O Kuja
- Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | | | - Rose A Marks
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | | | | | - Sadik Muzemil
- School of Life Science, University of Warwick, Coventry, UK
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Verena Ras
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa
| | - Yves H Tchiechoua
- Pan African University Institute for Basic Sciences Technology and Innovation, Nairobi, Kenya
| | | | - Krystal A Tolley
- South African National Biodiversity Institute, Claremont, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | | | - Ntanganedzeni Mapholi
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa
| | - Anne W T Muigai
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
- National Defense University-Kenya, Nakuru, Kenya.
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Edinburgh, UK.
- International Livestock Research Institute, Nairobi, Kenya.
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa.
| | - ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
- Early Cancer Institute, Department of Oncology, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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Tayimetha CY, Njunda LA, Akenji B, Founou RC, Feteh V, Zofou D, Chafa A, Oyono Y, Etogo B, Tseuko D, Fonkoua MC, Harrison OB. Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates from Yaoundé, Cameroon, 2019 to 2020. Microb Genom 2023; 9:mgen001091. [PMID: 37590058 PMCID: PMC10483411 DOI: 10.1099/mgen.0.001091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
This study investigated antimicrobial resistance (AMR) phenotypes and genotypes exhibited by Neisseria gonorrhoeae from Yaoundé, Cameroon. AMR to tetracycline, penicillin and ciprofloxacin was observed although none of the isolates had reduced susceptibility to azithromycin, cefixime or ceftriaxone. Whole genome sequence (WGS) data were obtained and, using a threshold of 300 or fewer locus differences in the N. gonorrhoeae core gene multilocus sequence typing (cgMLST) scheme, four distinct core genome lineages were identified. Publicly available WGS data from 1355 gonococci belonging to these four lineages were retrieved from the PubMLST database, allowing the Cameroonian isolates to be examined in the context of existing data and compared with related gonococci. Examination of AMR genotypes in this dataset found an association between the core genome and AMR with, for example, isolates belonging to the core genome group, Ng_cgc_300 : 21, possessing GyrA and ParC alleles with amino acid substitutions conferring high-level resistance to ciprofloxacin while lineages Ng_cgc_300 : 41 and Ng_cgc_300 : 243 were predicted to be susceptible to several antimicrobials. A core genome lineage, Ng_cgc_300 : 498, was observed which largely consisted of gonococci originating from Africa. Analyses from this study demonstrate the advantages of using the N. gonorrhoeae cgMLST scheme to find related gonococci to carry out genomic analyses that enhance our understanding of the population biology of this important pathogen.
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Affiliation(s)
- Carolle Yanique Tayimetha
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
- National Public Health Laboratory, Yaounde, Cameroon
| | | | - Blaise Akenji
- National Public Health Laboratory, Yaounde, Cameroon
| | - Raspail Carrel Founou
- Department of Microbiology, Haematology and Immunology of University of Dschang, Dschang, Cameroon
| | - Vitalis Feteh
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Denis Zofou
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Anicet Chafa
- Medical Bacteriology Laboratory of University Hospital Center, Yaoundé, Cameroon
| | - Yannick Oyono
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | | | - Dorine Tseuko
- National Public Health Laboratory, Yaounde, Cameroon
| | - Marie Christine Fonkoua
- Centre Pasteur du Cameroon, Yaoundé, Cameroon
- Cameroonian Society of Microbiology, Yaoundé, Cameroon
| | - Odile B. Harrison
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Peñaranda A, Pérez-Herrera LC, Gantiva M, Moreno-López S, Manrique J, Peñaranda D, García E. Factors associated with allergic rhinitis and combined allergic rhinitis and asthma syndrome (CARAS) in adults undergoing immunotherapy in a tropical country: Is ISAAC-III questionnaire useful in adult populations? Allergol Immunopathol (Madr) 2023; 51:78-86. [PMID: 37422783 DOI: 10.15586/aei.v51i4.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/30/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND Allergic diseases affect about 10-30% of the population in low- or middle-income tropical countries. Few studies describe the factors associated with allergic diseases in adult patients undergoing immunotherapy in Latin American countries. OBJECTIVE This study aimed to determine the factors associated with allergic rhinitis (AR) and AR in comorbidity with asthma (CARAS) in adults treated with immunotherapy in two allergy referral centers in Bogotá (Colombia). MATERIAL AND METHODS Observational, cross-sectional study conducted between January 2018 and January 2019. ISAAC-III and sociodemographic questionnaires were applied to determine the factors associated with AR and CARAS in adults treated with immunotherapy who attended the allergy consult at the Fundación Santa Fe de Bogotá and Unimeq-Orl. RESULTS Among 416 adults aged 18-68 years, 71.4% (n = 297) were women. Regarding the sensitization results obtained by skin prick test, the most frequent allergens were house dust mites (64.18%): 49.03% were positive for both Dermatophagoides pteronyssinus and Dermatophagoides farinae, while 28.61% were positive for Blomia tropicalis. Excluding house dust mites, the most frequent allergens were dog hair (31.01%), cat hair (15.1%), grasses (15.9%), and food (15.9%). The main factor associated with exclusive AR was regular acetaminophen use more than four times a year: Prevalence ratio (PR) = 1.77 (95% CI: 1.12-2.25). The main factor associated with CARAS was cesarean delivery PR: 1.44 (95% CI: 1.09-1.78). CONCLUSION The main factor associated with AR was regular acetaminophen use, while that associated with CARAS was cesarean delivery. The ISAAC-III questionnaire can be a useful low-cost tool to assess the factors associated with allergic diseases in adults in tropical countries.
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Affiliation(s)
- Augusto Peñaranda
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Departmen of Otolaryngology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
- Allergy and Otolaryngology Research Groups, UNIMEQ-ORL, Bogotá, Colombia
| | - Lucía C Pérez-Herrera
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Departmen of Otolaryngology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Manuela Gantiva
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Departmen of Otolaryngology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
- Section of Otolaryngology, Fundación Universitaria de Ciencias de la Salud - Hospital de San José, Bogotá, Colombia
| | - Sergio Moreno-López
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Departmen of Otolaryngology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Julian Manrique
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Allergy section, Department of Pediatrics, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Daniel Peñaranda
- Allergy and Otolaryngology Research Groups, UNIMEQ-ORL, Bogotá, Colombia
- Section of Otolaryngology, Fundación Universitaria de Ciencias de la Salud - Hospital de San José, Bogotá, Colombia
| | - Elizabeth García
- School of Medicine, Universidad de Los Andes, Bogotá, Colombia
- Departmen of Otolaryngology, Fundación Santa Fe de Bogotá, Bogotá, Colombia
- Section of Otolaryngology, Fundación Universitaria de Ciencias de la Salud - Hospital de San José, Bogotá, Colombia;
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Merten Cruz M, Sauvage T, Chariton A, de Freitas TRO. The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37060349 DOI: 10.1111/jfb.15406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.
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Affiliation(s)
- Marcelo Merten Cruz
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thomas Sauvage
- Programa de Pós-graduação em Ecologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anthony Chariton
- School of Life Sciences, Macquarie University, Sydney, Australia
| | - Thales Renato Ochotorena de Freitas
- Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Bi K, Herrera-Diestra JL, Bai Y, Du Z, Wang L, Gibson G, Johnson-Leon M, Fox SJ, Meyers LA. The risk of SARS-CoV-2 Omicron variant emergence in low and middle-income countries (LMICs). Epidemics 2023; 42:100660. [PMID: 36527867 PMCID: PMC9727964 DOI: 10.1016/j.epidem.2022.100660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 11/13/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
We estimated the probability of undetected emergence of the SARS-CoV-2 Omicron variant in 25 low and middle-income countries (LMICs) prior to December 5, 2021. In nine countries, the risk exceeds 50 %; in Turkey, Pakistan and the Philippines, it exceeds 99 %. Risks are generally lower in the Americas than Europe or Asia.
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Affiliation(s)
- Kaiming Bi
- The University of Texas at Austin, Austin, TX 78712, USA.
| | | | - Yuan Bai
- WHO Collaborating Center for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region of China
| | - Zhanwei Du
- WHO Collaborating Center for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region of China; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region of China
| | - Lin Wang
- University of Cambridge, Cambridge CB2 3EH, UK
| | - Graham Gibson
- The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Spencer J Fox
- The University of Texas at Austin, Austin, TX 78712, USA
| | - Lauren Ancel Meyers
- The University of Texas at Austin, Austin, TX 78712, USA; Santa Fe Institute, Santa Fe, NM, USA.
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Hudson LK, Andershock WE, Qian X, Gibbs PL, Orejuela K, Garman KN, Dunn JR, Denes TG. Phylogeny and Genomic Characterization of Clinical Salmonella enterica Serovar Newport Collected in Tennessee. Microbiol Spectr 2023; 11:e0387622. [PMID: 36602313 PMCID: PMC9927352 DOI: 10.1128/spectrum.03876-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 01/06/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Newport (S. Newport) is a clinically and epidemiologically significant serovar in the United States. It is the second most prevalent clinically isolated Salmonella serovar in the United States, and it can contaminate a wide variety of food products. In this study, we evaluated the population structure of S. Newport clinical isolates obtained by the Tennessee Department of Health during routine surveillance (n = 346), along with a diverse set of other global clinical isolates obtained from EnteroBase (n = 271). Most of these clinical isolates belonged to established lineages II and III. Additionally, we performed lineage-specific phylogenetic analyses and were able to identify 18 potential epidemiological clusters among the isolates from Tennessee, which represented a greater proportion of Tennessee isolates belonging to putative epidemiological clusters than the proportion of isolates of this serovar that are outbreak related. IMPORTANCE This study provides insight on the genomic diversity of one of the Salmonella serovars that most frequently cause human illness. Specifically, we explored the diversity of human clinical isolates from a localized region (Tennessee) and compared this level of diversity with the global context. Additionally, we showed that a greater proportion of isolates were associated with potential epidemiological clusters (based on genomic relatedness) than historical estimates. We also identified that one potential cluster was predicted to be multidrug resistant. Taken together, these findings provide insight on Salmonella enterica serovar Newport that can impact public health surveillance and responses and serve as a foundational context for the Salmonella research community.
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Affiliation(s)
- Lauren K. Hudson
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Xiaorong Qian
- Division of Laboratory Services, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Paula L. Gibbs
- Division of Laboratory Services, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Kelly Orejuela
- Tennessee Department of Health, Nashville, Tennessee, USA
| | | | - John R. Dunn
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Thomas G. Denes
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA
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20
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Dookie N, Ngema SL, Perumal R, Naicker N, Padayatchi N, Naidoo K. The Changing Paradigm of Drug-Resistant Tuberculosis Treatment: Successes, Pitfalls, and Future Perspectives. Clin Microbiol Rev 2022; 35:e0018019. [PMID: 36200885 PMCID: PMC9769521 DOI: 10.1128/cmr.00180-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) remains a global crisis due to the increasing incidence of drug-resistant forms of the disease, gaps in detection and prevention, models of care, and limited treatment options. The DR-TB treatment landscape has evolved over the last 10 years. Recent developments include the remarkable activity demonstrated by the newly approved anti-TB drugs bedaquiline and pretomanid against Mycobacterium tuberculosis. Hence, treatment of DR-TB has drastically evolved with the introduction of the short-course regimen for multidrug-resistant TB (MDR-TB), transitioning to injection-free regimens and the approval of the 6-month short regimens for rifampin-resistant TB and MDR-TB. Moreover, numerous clinical trials are under way with the aim to reduce pill burden and shorten the DR-TB treatment duration. While there have been apparent successes in the field, some challenges remain. These include the ongoing inclusion of high-dose isoniazid in DR-TB regimens despite a lack of evidence for its efficacy and the inclusion of ethambutol and pyrazinamide in the standard short regimen despite known high levels of background resistance to both drugs. Furthermore, antimicrobial heteroresistance, extensive cavitary disease and intracavitary gradients, the emergence of bedaquiline resistance, and the lack of biomarkers to monitor DR-TB treatment response remain serious challenges to the sustained successes. In this review, we outline the impact of the new drugs and regimens on patient treatment outcomes, explore evidence underpinning current practices on regimen selection and duration, reflect on the disappointments and pitfalls in the field, and highlight key areas that require continued efforts toward improving treatment approaches and rapid biomarkers for monitoring treatment response.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Senamile L. Ngema
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nikita Naicker
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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21
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Barua S, Bai J, Kelly PJ, Hanzlicek G, Noll L, Johnson C, Yin JH, Wang C. Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. Emerg Microbes Infect 2022; 11:14-17. [PMID: 34783635 PMCID: PMC8725927 DOI: 10.1080/22221751.2021.2007738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/14/2021] [Indexed: 11/02/2022]
Abstract
Knowledge of SARS-CoV-2 variants is essential for formulating effective control policies. Currently, variants are only identified in relatively small percentages of cases as the required genome sequencing is expensive, time-consuming, and not always available. In countries with facilities to sequence the SARS-CoV-2, the Delta variant currently predominates. Elsewhere, the prevalence of the Delta variant is unclear. To avoid the need for sequencing, we investigated a RT-FRET-PCR that could detect all SARS-CoV-2 strains and simultaneously identify the Delta variant. The established Delta RT-FRET-PCR was performed on reference SARS-CoV-2 strains, and human nasal swab samples positive for the Delta and non-Delta strains. The Delta RT-FRET-PCR established in this study detected as few as ten copies of the DNA target and 100 copies of RNA target per reaction. Melting points of products obtained with SARS-CoV-2 Delta variants (around 56.1°C) were consistently higher than products obtained with non-Delta strains (around 52.5°C). The Delta RT-FRET-PCR can be used to diagnose COVID-19 patients and simultaneously identify if they are infected with the Delta variant. The Delta RT-FRET-PCR can be performed with all major thermocycler brands meaning data on Delta variant can now be readily generated in diagnostic laboratories worldwide.
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Affiliation(s)
- Subarna Barua
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Patrick John Kelly
- Department of Veterinary Clinical Sciences, Ross University School of Veterinary Medicine, St. Kitts & Nevis
| | - Gregg Hanzlicek
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Calvin Johnson
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Ji-Hang Yin
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Chengming Wang
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
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22
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Kennedy CRM, de Bruin YB, Lequarré AS, Ackerman RT, Luster J, Tsang TM, McInturff KD, Carter CP, Pilch R. One Health security lessons from a year-long webinar series on international COVID-19 response. ONE HEALTH OUTLOOK 2022; 4:15. [PMID: 36209267 PMCID: PMC9547628 DOI: 10.1186/s42522-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Following the principles outlined by the Global Outbreak Alert and Response Network, the Federal Bureau of Investigation's International Biosecurity and Prevention Forum, the European Commission's Joint Research Centre, and the Middlebury Institute of International Studies' James Martin Center for Nonproliferation Studies cohosted a webinar series from April 2020 to January 2021 on COVID-19 management across Africa, Europe, and North America. We provide here an overview of the webinar series and discuss how lessons learned during the COVID-19 pandemic and debated during the webinars can be used to bridge One Health with biological threat-driven health security. This report can be used to inform recommendations for future One Health security approaches to strengthen global capacity and multidisciplinary cooperation.
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Affiliation(s)
| | - Yuri Bruinen de Bruin
- Joint Research Centre, Directorate for Space, European Commission, Security, and Migration, Geel, Belgium and Ispra, Italy.
| | - Anne-Sophie Lequarré
- Joint Research Centre, Directorate for Space, European Commission, Security, and Migration, Geel, Belgium and Ispra, Italy
| | | | - Jill Luster
- Middlebury Institute of International Studies, James Martin Centre for Nonproliferation Studies, Monterey, California, USA
| | | | | | | | - Richard Pilch
- Middlebury Institute of International Studies, James Martin Centre for Nonproliferation Studies, Monterey, California, USA
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23
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Xiaoli L, Hagey JV, Park DJ, Gulvik CA, Young EL, Alikhan NF, Lawsin A, Hassell N, Knipe K, Oakeson KF, Retchless AC, Shakya M, Lo CC, Chain P, Page AJ, Metcalf BJ, Su M, Rowell J, Vidyaprakash E, Paden CR, Huang AD, Roellig D, Patel K, Winglee K, Weigand MR, Katz LS. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics. PeerJ 2022; 10:e13821. [PMID: 36093336 PMCID: PMC9454940 DOI: 10.7717/peerj.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/08/2022] [Indexed: 01/18/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.
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Affiliation(s)
- Lingzi Xiaoli
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jill V. Hagey
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Christopher A. Gulvik
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Erin L. Young
- Utah Public Health Laboratory, Salt Lake City, UT, United States of America
| | | | - Adrian Lawsin
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Norman Hassell
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Kristen Knipe
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Kelly F. Oakeson
- Utah Public Health Laboratory, Salt Lake City, UT, United States of America
| | - Adam C. Retchless
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Patrick Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Benjamin J. Metcalf
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Michelle Su
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jessica Rowell
- SARS-CoV-2 Emerging Variant Sequencing Project Dry Lab Group Laboratory and Testing Task Force COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Eshaw Vidyaprakash
- SARS-CoV-2 Emerging Variant Sequencing Project Dry Lab Group Laboratory and Testing Task Force COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Clinton R. Paden
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Andrew D. Huang
- SARS-CoV-2 Emerging Variant Sequencing Project Dry Lab Group Laboratory and Testing Task Force COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Dawn Roellig
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ketan Patel
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Kathryn Winglee
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Michael R. Weigand
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Lee S. Katz
- Strain Surveillance and Emerging Variant Team, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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24
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Examining Barriers and Opportunities of Conducting Genome-Wide Association Studies in Developing Countries. CURR EPIDEMIOL REP 2022. [DOI: 10.1007/s40471-022-00303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Yek C, Pacheco AR, Vanaerschot M, Bohl JA, Fahsbender E, Aranda-Díaz A, Lay S, Chea S, Oum MH, Lon C, Tato CM, Manning JE. Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead. FRONTIERS IN EPIDEMIOLOGY 2022; 2:926695. [PMID: 36247976 PMCID: PMC9558322 DOI: 10.3389/fepid.2022.926695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.
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Affiliation(s)
- Christina Yek
- Department of Critical Care Medicine, National Institutes of Health Clinical Center, Bethesda, MD, United States
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Andrea R. Pacheco
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jennifer A. Bohl
- Vaccine Immunology Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | | | - Andrés Aranda-Díaz
- Chan Zuckerberg Initiative, Redwood City, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Sreyngim Lay
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Meng Heng Oum
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Chanthap Lon
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jessica E. Manning
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
- International Center of Excellence in Research, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
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26
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Hercules SM, Liu X, Bassey-Archibong BBI, Skeete DHA, Smith Connell S, Daramola A, Banjo AA, Ebughe G, Agan T, Ekanem IO, Udosen J, Obiorah C, Ojule AC, Misauno MA, Dauda AM, Egbujo EC, Hercules JC, Ansari A, Brain I, MacColl C, Xu Y, Jin Y, Chang S, Carpten JD, Bédard A, Pond GR, Blenman KRM, Manojlovic Z, Daniel JM. Analysis of the genomic landscapes of Barbadian and Nigerian women with triple negative breast cancer. Cancer Causes Control 2022; 33:831-841. [PMID: 35384527 PMCID: PMC9085672 DOI: 10.1007/s10552-022-01574-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/12/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that disproportionately affects women of African ancestry (WAA) and is often associated with poor survival. Although there is a high prevalence of TNBC across West Africa and in women of the African diaspora, there has been no comprehensive genomics study to investigate the mutational profile of ancestrally related women across the Caribbean and West Africa. METHODS This multisite cross-sectional study used 31 formalin-fixed paraffin-embedded (FFPE) samples from Barbadian and Nigerian TNBC participants. High-resolution whole exome sequencing (WES) was performed on the Barbadian and Nigerian TNBC samples to identify their mutational profiles and comparisons were made to African American, European American and Asian American sequencing data obtained from The Cancer Genome Atlas (TCGA). Whole exome sequencing was conducted on tumors with an average of 382 × coverage and 4335 × coverage for pooled germline non-tumor samples. RESULTS Variants detected at high frequency in our WAA cohorts were found in the following genes NBPF12, PLIN4, TP53 and BRCA1. In the TCGA TNBC cases, these genes had a lower mutation rate, except for TP53 (32% in our cohort; 63% in TCGA-African American; 67% in TCGA-European American; 63% in TCGA-Asian). For all altered genes, there were no differences in frequency of mutations between WAA TNBC groups including the TCGA-African American cohort. For copy number variants, high frequency alterations were observed in PIK3CA, TP53, FGFR2 and HIF1AN genes. CONCLUSION This study provides novel insights into the underlying genomic alterations in WAA TNBC samples and shines light on the importance of inclusion of under-represented populations in cancer genomics and biomarker studies.
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Affiliation(s)
- Shawn M. Hercules
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
| | - Xiyu Liu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | | | - Desiree H. A. Skeete
- African Caribbean Cancer Consortium, Philadelphia, PA USA
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Pathology, Queen Elizabeth Hospital, Bridgetown, Barbados
| | - Suzanne Smith Connell
- grid.412886.10000 0004 0592 769XFaculty of Medical Sciences, University of the West Indies at Cave Hill, Bridgetown, Barbados
- grid.415521.60000 0004 0570 5165Department of Radiation Oncology, Queen Elizabeth Hospital, Bridgetown, Barbados
- Present Address: Cancer Specialists Inc, Bridgetown, Barbados
| | - Adetola Daramola
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Adekunbiola A. Banjo
- grid.411283.d0000 0000 8668 7085Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Godwin Ebughe
- grid.413097.80000 0001 0291 6387Department of Pathology, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Thomas Agan
- grid.413097.80000 0001 0291 6387Department of Obstetrics & Gynaecology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Ima-Obong Ekanem
- grid.413097.80000 0001 0291 6387Department of Pathology, College of Medical Sciences, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Joe Udosen
- grid.413097.80000 0001 0291 6387Division of General and Breast Surgery, University of Calabar Teaching Hospital, Calabar, Nigeria
| | - Christopher Obiorah
- grid.412738.bDepartment of Anatomical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Aaron C. Ojule
- grid.412738.bDepartment of Chemical Pathology, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | - Michael A. Misauno
- grid.411946.f0000 0004 1783 4052Department of Surgery, Jos University Teaching Hospital, Jos, Nigeria
| | - Ayuba M. Dauda
- grid.411946.f0000 0004 1783 4052Department of Pathology, Jos University Teaching Hospital, Jos, Nigeria
| | | | - Jevon C. Hercules
- grid.12916.3d0000 0001 2322 4996Department of Mathematics, University of the West Indies at Mona, Kingston, Jamaica
- grid.12955.3a0000 0001 2264 7233Present Address: Wang Yanan Institute for Studies in Economics, Xiamen University, Xiamen, China
| | - Amna Ansari
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Ian Brain
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Christine MacColl
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Yili Xu
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Yuxin Jin
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Sharon Chang
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - John D. Carpten
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - André Bédard
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
| | - Greg R. Pond
- grid.25073.330000 0004 1936 8227Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON Canada
| | - Kim R. M. Blenman
- grid.433818.5Department of Internal Medicine, Section of Medical Oncology, Yale Cancer Center, School of Medicine, New Haven, CT USA
- grid.47100.320000000419368710Department of Computer Science, School of Engineering and Applied Science, Yale University, New Haven, CT USA
| | - Zarko Manojlovic
- grid.42505.360000 0001 2156 6853Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Juliet M. Daniel
- grid.25073.330000 0004 1936 8227Department of Biology, McMaster University, Hamilton, ON Canada
- African Caribbean Cancer Consortium, Philadelphia, PA USA
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Jaffal L, Mrad Z, Ibrahim M, Salami A, Audo I, Zeitz C, El Shamieh S. The research output of rod-cone dystrophy genetics. Orphanet J Rare Dis 2022; 17:175. [PMID: 35461258 PMCID: PMC9034540 DOI: 10.1186/s13023-022-02318-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
Non-syndromic rod-cone dystrophy (RCD) is the most common condition in inherited retinal diseases. The aim of this study was to evaluate the research output and productivity related to RCD genetics per countries as classified by the human development index (HDI), by analyzing publication frequency and citations, the choice of journals and publishers, since 2000 to date. We have also analyzed the use of next-generation sequencing (NGS) in publications originating from countries with different HDIs. One thousand four hundred articles focusing on non-syndromic RCD were downloaded and analyzed. Citations and published articles were adjusted per one million individuals. The research output is significantly higher in very high HDI countries (86% of the total publications and 95% of the citations) than countries with lower HDIs in all aspects. High and medium HDI countries published together 13.6% of the total articles worldwide and received 4.6% of the citations. On the publication level, the USA (26%), United Kingdom (10%), and Japan (7%) were the top 3 among very high HDI countries, while China (6%) and India (2%) ranked first in high and medium HDI countries respectively. On the citation level, similar profiles were found. Following adjustment for population size, Switzerland (~14%), Jordan (~ 1%) and Morocco (<0.2%) showed the highest rates of publications in very high, high and medium HDI countries respectively. Very high HDI countries published 71% of their papers in first quartile journals (first quartile in Scimago journal rank; Q1), and 23% in Q2 journals. High and medium HDI countries showed a similar profile in quartiles with ~ 40% of their papers published in Q1 journals and ~ 30% in Q2 journals. The first publication using NGS was issued in 2009 in very high HDI countries, while it appeared in 2012 in high HDI countries, and in 2017 in medium HDI countries, with a respective lag of 3 to 8 years compared to very high HDI countries. A profound gap exists between very high HDI countries and the rest of the world. To fill it in, we propose implementing NGS, supporting international collaborations, building capacities and infrastructures, improving accessibility of patients to services, and increasing national and international funding.
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Affiliation(s)
- Lama Jaffal
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Zamzam Mrad
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Ali Salami
- Department of Mathematics, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, Paris, France.,CHNO Des Quinze-Vingts, INSERM-DGOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, UK
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, Paris, France
| | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:genes13030452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Estrela PFN, dos Santos CA, Resende PC, Lima PM, da Silva TDSC, Saboia-Vahia L, Siqueira MM, Silveira-Lacerda EDP, Duarte GRM. Fast, low-cost and highly specific colorimetric RT-LAMP assays for inference of SARS-CoV-2 Omicron BA.1 and BA.2 lineages. Analyst 2022; 147:5613-5622. [DOI: 10.1039/d2an01625g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The RT-LAMP assays can quickly and cheaply infer and distinguish colorimetrically two lineages (BA.1 and BA.2) of the Omicron variant, enabling the rationalization of genetic sequencing.
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Affiliation(s)
- Paulo Felipe Neves Estrela
- Laboratório de Biomicrofluídica – Instituto de Química – Universidade Federal de Goiás, 74690-900, Goiânia, GO, Brazil
| | - Carlos Abelardo dos Santos
- Laboratório de Genética Molecular e Citogenética – Instituto de Ciências Biológicas – Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Patricia Mayer Lima
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Thauane dos Santos Correia da Silva
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Leonardo Saboia-Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Reference Laboratory for COVID-19 (WHO), 21040-360, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Elisângela de Paula Silveira-Lacerda
- Laboratório de Genética Molecular e Citogenética – Instituto de Ciências Biológicas – Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil
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Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T Goolam Mahomed
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R P H Peters
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Foundation for Professional Development, Research Unit, East London, South Africa
| | - M Allam
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A Ismail
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S Mtshali
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V Ueckermann
- Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa.
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Munung NS, de Vries J, Pratt B. Genomics governance: advancing justice, fairness and equity through the lens of the African communitarian ethic of Ubuntu. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2021; 24:377-388. [PMID: 33797712 PMCID: PMC8349790 DOI: 10.1007/s11019-021-10012-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/19/2021] [Indexed: 05/18/2023]
Abstract
There is growing interest for a communitarian approach to the governance of genomics, and for such governance to be grounded in principles of justice, equity and solidarity. However, there is a near absence of conceptual studies on how communitarian-based principles, or values, may inform, support or guide the governance of genomics research. Given that solidarity is a key principle in Ubuntu, an African communitarian ethic and theory of justice, there is emerging interest about the extent to which Ubuntu could offer guidance for the governance of genomics research in Africa. To this effect, we undertook a conceptual analysis of Ubuntu with the goal of identifying principles that could inform equity-oriented governance of genomics research. Solidarity, reciprocity, open sharing, accountability, mutual trust, deliberative decision-making and inclusivity were identified as core principles that speak directly to the different macro-level ethical issues in genomics research in Africa such as: the exploitation of study populations and African researchers, equitable access and use of genomics data, benefit sharing, the possibility of genomics to widen global health inequities and the fair distribution of resources such as intellectual property and patents. We use the identified the principles to develop ethical guidance for genomics governance in Africa.
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Affiliation(s)
- Nchangwi Syntia Munung
- Department of Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jantina de Vries
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Bridget Pratt
- Centre for Health Equity, School of Population and Global Health, University of Melbourne, Melbourne, Australia
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A cloth-based hybridization array system for rapid detection of the food- and waterborne protozoan parasites Giardia duodenalis, Cryptosporidium spp. and Toxoplasma gondii. Food Waterborne Parasitol 2021; 24:e00130. [PMID: 34458600 PMCID: PMC8379661 DOI: 10.1016/j.fawpar.2021.e00130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/17/2023] Open
Abstract
Protozoan parasites in food or water samples are generally detected using microscopy or PCR followed by Sanger sequencing. However, microscopy is subjective, requires a high degree of expertise and has limited sensitivity, while DNA sequencing requires expensive and specialized equipment and facilities. This study describes a cloth-based hybridization array system (CHAS) that is an alternative to Sanger sequencing to confirm PCR-positive samples. CHAS is an inexpensive, rapid and reliable method for the simultaneous detection of multiple protozoan parasite species based on the colorimetric detection of PCR amplicons on a polyester cloth. PCR primers and CHAS hybridization probes were developed to detect the protozoan parasites Giardia duodenalis, Cryptosporidium spp. and Toxoplasma gondii. In addition, CHAS probes were designed for the differentiation of G. duodenalis Assemblages A and B. In artificially contaminated fresh produce (lettuce, parsley) and water samples (river water, wastewater), this CHAS assay allowed for the successful detection of G. duodenalis, Cryptosporidium spp., and T. gondii. The present study demonstrates that the CHAS detection method is a simple and inexpensive alternative to DNA sequencing for the confirmation of PCR-positive results in laboratories testing for parasites in food or water samples. This assay may also be beneficial in developing countries, where DNA sequencing facilities may not be readily available.
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Yates J, Gutiérrez-Sacristán A, Jouhet V, LeBlanc K, Esteves C, DeSain TN, Benik N, Stedman J, Palmer N, Mellon G, Kohane I, Avillach P. Finding commonalities in rare diseases through the undiagnosed diseases network. J Am Med Inform Assoc 2021; 28:1694-1702. [PMID: 34009343 PMCID: PMC8324228 DOI: 10.1093/jamia/ocab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Objective When studying any specific rare disease, heterogeneity and scarcity of affected individuals has historically hindered investigators from discerning on what to focus to understand and diagnose a disease. New nongenomic methodologies must be developed that identify similarities in seemingly dissimilar conditions. Materials and Methods This observational study analyzes 1042 patients from the Undiagnosed Diseases Network (2015-2019), a multicenter, nationwide research study using phenotypic data annotated by specialized staff using Human Phenotype Ontology terms. We used Louvain community detection to cluster patients linked by Jaccard pairwise similarity and 2 support vector classifier to assign new cases. We further validated the clusters’ most representative comorbidities using a national claims database (67 million patients). Results Patients were divided into 2 groups: those with symptom onset before 18 years of age (n = 810) and at 18 years of age or older (n = 232) (average symptom onset age: 10 [interquartile range, 0-14] years). For 810 pediatric patients, we identified 4 statistically significant clusters. Two clusters were characterized by growth disorders, and developmental delay enriched for hypotonia presented a higher likelihood of diagnosis. Support vector classifier showed 0.89 balanced accuracy (0.83 for Human Phenotype Ontology terms only) on test data. Discussions To set the framework for future discovery, we chose as our endpoint the successful grouping of patients by phenotypic similarity and provide a classification tool to assign new patients to those clusters. Conclusion This study shows that despite the scarcity and heterogeneity of patients, we can still find commonalities that can potentially be harnessed to uncover new insights and targets for therapy.
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Affiliation(s)
- Josephine Yates
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Vianney Jouhet
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Thomas N DeSain
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nick Benik
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason Stedman
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathan Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Guillaume Mellon
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Corresponding Author: Paul Avillach, MD, PhD, 10 Shattuck Street, 02115 Boston, MA, USA;
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Vogel M, Utpatel C, Corbett C, Kohl TA, Iskakova A, Ahmedov S, Antonenka U, Dreyer V, Ibrahimova A, Kamarli C, Kosimova D, Mohr V, Sahalchyk E, Sydykova M, Umetalieva N, Kadyrov A, Kalmambetova G, Niemann S, Hoffmann H. Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country. Sci Rep 2021; 11:15333. [PMID: 34321545 PMCID: PMC8319420 DOI: 10.1038/s41598-021-94297-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/06/2021] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project's timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.
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Affiliation(s)
- Monica Vogel
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Caroline Corbett
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Altyn Iskakova
- Republican Tuberculosis Reference Laboratory, Bishkek, Kyrgyz Republic
| | - Sevim Ahmedov
- USAID, Bureau for Global Health, TB Division, Washington, DC, USA
| | - Uladzimir Antonenka
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Ainura Ibrahimova
- ABT Associates, Defeat TB Project Management, Bishkek, Kyrgyz Republic
| | | | - Dilorom Kosimova
- ABT Associates, Defeat TB Project Management, Bishkek, Kyrgyz Republic
| | - Vanessa Mohr
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Evgeni Sahalchyk
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany
| | - Meerim Sydykova
- Republican Tuberculosis Reference Laboratory, Bishkek, Kyrgyz Republic
| | - Nagira Umetalieva
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany
| | - Abdylat Kadyrov
- Republican Tuberculosis Center, National Tuberculosis Project Management, Bishkek, Kyrgyz Republic
| | | | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, Department IML Red GmbH, WHO - Supranational Tuberculosis Reference Laboratory Munich-Gauting, Robert Koch-Allee 2, 82131, Gauting, Germany.
- SYNLAB Gauting, SYNLAB Human Genetics, Munich-Gauting, Germany.
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Thongjued K, Chotigeat W, Bumrungsri S, Thanakiatkrai P, Kitpipit T. Direct PCR-DGGE Technique Reveals Wrinkle-Lipped Free-Tailed Bat (Chaerephon plicatus Buchanan, 1800) Predominantly Consume Planthoppers and Mosquitoes in Central Thailand. ACTA CHIROPTEROLOGICA 2021. [DOI: 10.3161/15081109acc2021.23.1.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kantima Thongjued
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Wilaiwan Chotigeat
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Sara Bumrungsri
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Phuvadol Thanakiatkrai
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
| | - Thitika Kitpipit
- Prince of Songkla University, 15 Karnchanawanich Road, Hat Yai, Songkhla, Thailand 90112
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Guzel F, Romano M, Keles E, Piskin D, Ozen S, Poyrazoglu H, Kasapcopur O, Demirkaya E. Next Generation Sequencing Based Multiplex Long-Range PCR for Routine Genotyping of Autoinflammatory Disorders. Front Immunol 2021; 12:666273. [PMID: 34177904 PMCID: PMC8219981 DOI: 10.3389/fimmu.2021.666273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
Background During the last decade, remarkable progress with massive sequencing has been made in the identification of disease-associated genes for AIDs using next-generation sequencing technologies (NGS). An international group of experts described the ideal genetic screening method which should give information about SNVs, InDels, Copy Number Variations (CNVs), GC rich regions. We aimed to develop and validate a molecular diagnostic method in conjunction with the NGS platform as an inexpensive, extended and uniform coverage and fast screening tool which consists of nine genes known to be associated with various AIDs. Methods For the validation of basic and expanded panels, long-range multiplex models were setup on healthy samples without any known variations for MEFV, MVK, TNFRSF1A, NLRP3, PSTPIP1, IL1RN, NOD2, NLRP12 and LPIN2 genes. Patients with AIDs who had already known causative variants in these genes were sequenced for analytical validation. As a last step, multiplex models were validated on patients with pre-diagnosis of AIDs. All sequencing steps were performed on the Illumina NGS platform. Validity steps included the selection of related candidate genes, primer design, development of screening methods, validation and verification of the product. The GDPE (Gentera) bioinformatics pipeline was followed. Results Although there was no nonsynonymous variation in 21 healthy samples, 107 synonymous variant alleles and some intronic and UTR variants were detected. In 10 patients who underwent analytical validation, besides the 11 known nonsynonymous variant alleles, 11 additional nonsynonymous variant alleles and a total of 81 synonymous variants were found. In the clinical validation phase, 46 patients sequenced with multiplex panels, genetic and clinical findings were combined for diagnosis. Conclusion In this study, we describe the development and validation of an NGS-based multiplex array enabling the "long-amplicon" approach for targeted sequencing of nine genes associated with common AIDs. This screening tool is less expensive and more comprehensive compared to other methods and more informative than traditional sequencing. The proposed panel offers advantages to WES or hybridization probe equivalents in terms of CNV analysis, high sensitivity and uniformity, GC-rich region sequencing, InDel detection and intron covering.
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Affiliation(s)
- Ferhat Guzel
- Department of Research and Development, Gentera Biotechnology, Istanbul, Turkey
| | - Micol Romano
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Erdi Keles
- Department of Research and Development, Gentera Biotechnology, Istanbul, Turkey
| | - David Piskin
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Seza Ozen
- Department of Paediatrics, Division of Paediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Hakan Poyrazoglu
- Department of Paediatrics, Division of Paediatric Rheumatology, Erciyes University, Kayseri, Turkey
| | - Ozgur Kasapcopur
- Department of Paediatrics, Division of Paediatric Rheumatology, Cerrhapasa Medical School, Istanbul University, Istanbul, Turkey
| | - Erkan Demirkaya
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
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Alam I, Kamau AA, Ngugi DK, Gojobori T, Duarte CM, Bajic VB. KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data. Sci Rep 2021; 11:11511. [PMID: 34075103 PMCID: PMC8169707 DOI: 10.1038/s41598-021-90799-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require acceess to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data. We illustrate the capacities KMAP provides through the re-assembly of ~ 27,000 public metagenomic samples captured in ~ 450 studies sampled across ~ 77 diverse habitats. A small subset of these metagenomic assemblies is used in this pilot study grouped into 36 new habitat-specific gene catalogs, all based on full-length (complete) genes. Extensive taxonomic and gene annotations are stored in Gene Information Tables (GITs), a simple tractable data integration format useful for analysis through command line or for database management. KMAP pilot study provides the exploration and comparison of microbial GITs across different habitats with over 275 million genes. KMAP access to data and analyses is available at https://www.cbrc.kaust.edu.sa/aamg/kmap.start .
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Affiliation(s)
- Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Allan Anthony Kamau
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - David Kamanda Ngugi
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Red Sea Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Hulaniuk ML, Corach D, Trinks J, Caputo M. A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension. Lett Appl Microbiol 2021; 73:308-317. [PMID: 34048079 DOI: 10.1111/lam.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022]
Abstract
Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.
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Affiliation(s)
- M L Hulaniuk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - D Corach
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
| | - J Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Caputo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
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Rotimi SO, Rotimi OA, Salhia B. Authorship Patterns in Cancer Genomics Publications Across Africa. JCO Glob Oncol 2021; 7:747-755. [PMID: 34033494 PMCID: PMC8457814 DOI: 10.1200/go.20.00552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/26/2021] [Accepted: 03/31/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Authorship is a proxy indicator of research capacity. Understanding the research capacity is imperative for developing population-specific cancer control strategies. This is particularly apropos for African nations, where mortality from cancer is projected to surpass that from infectious disease and the populations are critically under-represented in cancer and genomics studies. Here, we present an analysis and discussion of the patterns of authorship in Africa as they pertain to cancer genomics research across African countries. METHODS PubMed metadata of relevant cancer genomics peer-reviewed publications on African populations, published between January 1, 1990, and December 31, 2019, were retrieved and analyzed for patterns of authorship affiliation using R packages, RISmed, and Pubmed.mineR. RESULTS The data showed that only 0.016% (n = 375) of cancer publications globally were on cancer genomics of African people. More than 50% of the first and last authors of these publications originated from the North African countries of Tunisia, Morocco, Egypt, and Algeria. South Africa (13.6% and 12.7%) and Nigeria (2.2% and 1.9%) were the Sub-Saharan African countries most represented by first and last authorship positions, respectively. The United States contributed 12.6% of first and last authored papers, and nearly 50% of all African countries had no contributing author for the publications we reviewed. CONCLUSION This study highlights and brings awareness to the paucity of cancer genomics research on African populations and by African authors and identifies a need for concerted efforts to encourage and enable more research in Africa, needed for achieving global equity in cancer outcomes.
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Affiliation(s)
- Solomon O. Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Oluwakemi A. Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Centre, Los Angeles, CA
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Genotyping of the Major SARS-CoV-2 Clade by Short-Amplicon High-Resolution Melting (SA-HRM) Analysis. Genes (Basel) 2021; 12:genes12040531. [PMID: 33916492 PMCID: PMC8067340 DOI: 10.3390/genes12040531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022] Open
Abstract
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
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Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:213-233. [PMID: 33794662 PMCID: PMC8060717 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Chiamaka Jessica Okeke
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maureen Bilinga Tendwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz–Sidi Mohammed Ben Abdellah University, Fez, Morocco
- University of Mohamed Premier, Oujda, Morocco
| | - Reem Mohamed Sallam
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Suez, Egypt
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Michael Turkson
- The National Institute for Mathematical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Faisal Mohamed Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samar Kamal Kassim
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Sylverken AA, El-Duah P, Owusu M, Schneider J, Yeboah R, Ayisi-Boateng NK, Gorman R, Adu E, Kwarteng A, Frimpong M, Binger T, Aryeetey S, Asamoah JA, Amoako YA, Amuasi JH, Beheim-Schwarzbach J, Owusu-Dabo E, Adu-Sarkodie Y, Obiri-Danso K, Corman VM, Drosten C, Phillips R. Transmission of SARS-CoV-2 in northern Ghana: insights from whole-genome sequencing. Arch Virol 2021; 166:1385-1393. [PMID: 33723631 PMCID: PMC7959303 DOI: 10.1007/s00705-021-04986-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.
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Affiliation(s)
- Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Philip El-Duah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Julia Schneider
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richmond Yeboah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | | | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Eric Adu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Alexander Kwarteng
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Jesse Addo Asamoah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Yaw Ampem Amoako
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Humphrey Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Ellis Owusu-Dabo
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Victor Max Corman
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Bernaola L, Darlington M, Britt K, Prade P, Roth M, Pekarcik A, Boone M, Ricke D, Tran A, King J, Carruthers K, Thompson M, Ternest JJ, Anderson SE, Gula SW, Hauri KC, Pecenka JR, Grover S, Puri H, Vakil SG. Technological Advances to Address Current Issues in Entomology: 2020 Student Debates. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:18. [PMID: 33908604 PMCID: PMC8080135 DOI: 10.1093/jisesa/ieab025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The 2020 Student Debates of the Entomological Society of America (ESA) were live-streamed during the Virtual Annual Meeting to debate current, prominent entomological issues of interest to members. The Student Debates Subcommittee of the National ESA Student Affairs Committee coordinated the student efforts throughout the year and hosted the live event. This year, four unbiased introductory speakers provided background for each debate topic while four multi-university teams were each assigned a debate topic under the theme 'Technological Advances to Address Current Issues in Entomology'. The two debate topics selected were as follows: 1) What is the best taxonomic approach to identify and classify insects? and 2) What is the best current technology to address the locust swarms worldwide? Unbiased introduction speakers and debate teams began preparing approximately six months before the live event. During the live event, teams shared their critical thinking and practiced communication skills by defending their positions on either taxonomical identification and classification of insects or managing the damaging outbreaks of locusts in crops.
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Affiliation(s)
- Lina Bernaola
- Department of Entomology, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Molly Darlington
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Kadie Britt
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Patricia Prade
- Department of Entomology and Nematology, University of Florida, Fort Pierce, FL 34945, USA
| | - Morgan Roth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Adrian Pekarcik
- Department of Entomology, The Ohio State University, Wooster, OH 44691, USA
| | - Michelle Boone
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Dylan Ricke
- Department of Entomology, The Ohio State University, Wooster, OH 44691, USA
| | - Anh Tran
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Joanie King
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Kelly Carruthers
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Morgan Thompson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - John J Ternest
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Sarah E Anderson
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Scott W Gula
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - Kayleigh C Hauri
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Jacob R Pecenka
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
| | - Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Heena Puri
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Surabhi Gupta Vakil
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Yinda CK, Seifert SN, Macmenamin P, van Doremalen N, Kim L, Bushmaker T, de Wit E, Quinones M, Munster VJ. A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform. J Infect Dis 2021; 221:S383-S388. [PMID: 31784761 DOI: 10.1093/infdis/jiz576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viruses in the genus Henipavirus encompass 2 highly pathogenic emerging zoonotic pathogens, Hendra virus (HeV) and Nipah virus (NiV). Despite the impact on human health, there is currently limited full-genome sequence information available for henipaviruses. This lack of full-length genomes hampers our ability to understand the molecular drivers of henipavirus emergence. Furthermore, rapidly deployable viral genome sequencing can be an integral part of outbreak response and epidemiological investigations to study transmission chains. In this study, we describe the development of a reverse-transcription, long-range polymerase chain reaction (LRPCR) assay for efficient genome amplification of NiV, HeV, and a related non-pathogenic henipavirus, Cedar virus (CedPV). We then demonstrated the utility of our method by amplifying partial viral genomes from 6 HeV-infected tissue samples from Syrian hamsters and 4 tissue samples from a NiV-infected African green monkey with viral loads as low as 52 genome copies/mg. We subsequently sequenced the amplified genomes on the portable Oxford Nanopore MinION platform and analyzed the data using a newly developed field-deployable bioinformatic pipeline. Our LRPCR assay allows amplification and sequencing of 2 or 4 amplicons in semi-nested reactions. Coupled with an easy-to-use bioinformatics pipeline, this method is particularly useful in the field during outbreaks in resource-poor environments.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Stephanie N Seifert
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Philip Macmenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Emmie de Wit
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mariam Quinones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Vincent J Munster
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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McInerney-Leo AM, Duncan EL. Massively Parallel Sequencing for Rare Genetic Disorders: Potential and Pitfalls. Front Endocrinol (Lausanne) 2021; 11:628946. [PMID: 33679611 PMCID: PMC7933540 DOI: 10.3389/fendo.2020.628946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
There have been two major eras in the history of gene discovery. The first was the era of linkage analysis, with approximately 1,300 disease-related genes identified by positional cloning by the turn of the millennium. The second era has been powered by two major breakthroughs: the publication of the human genome and the development of massively parallel sequencing (MPS). MPS has greatly accelerated disease gene identification, such that disease genes that would have taken years to map previously can now be determined in a matter of weeks. Additionally, the number of affected families needed to map a causative gene and the size of such families have fallen: de novo mutations, previously intractable by linkage analysis, can be identified through sequencing of the parent-child trio, and genes for recessive disease can be identified through MPS even of a single affected individual. MPS technologies include whole exome sequencing (WES), whole genome sequencing (WGS), and panel sequencing, each with their strengths. While WES has been responsible for most gene discoveries through MPS, WGS is superior in detecting copy number variants, chromosomal rearrangements, and repeat-rich regions. Panels are commonly used for diagnostic purposes as they are extremely cost-effective and generate manageable quantities of data, with no risk of unexpected findings. However, in instances of diagnostic uncertainty, it can be challenging to choose the right panel, and in these circumstances WES has a higher diagnostic yield. MPS has ethical, social, and legal implications, many of which are common to genetic testing generally but amplified due to the magnitude of data (e.g., relationship misattribution, identification of variants of uncertain significance, and genetic discrimination); others are unique to WES and WGS technologies (e.g., incidental or secondary findings). Nonetheless, MPS is rapidly translating into clinical practice as an extremely useful part of the clinical armamentarium.
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Affiliation(s)
- Aideen M. McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Emma L. Duncan
- Department of Twin Research & Genetic Epidemiology, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King’s College London, London, United Kingdom
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Mboowa G, Sserwadda I, Aruhomukama D. Genomics and bioinformatics capacity in Africa: no continent is left behind. Genome 2021; 64:503-513. [PMID: 33433259 DOI: 10.1139/gen-2020-0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda.,Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda.,The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Disease Institute, Makerere University, P.O. Box 22418, Kampala, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda
| | - Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
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Ibaba JD, Gubba A. High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1376. [PMID: 33081084 PMCID: PMC7602839 DOI: 10.3390/plants9101376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.
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Affiliation(s)
- Jacques Davy Ibaba
- Discipline of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, Agriculture Campus, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa;
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Rivière E, Heupink TH, Ismail N, Dippenaar A, Clarke C, Abebe G, Heusden P, Warren R, Meehan CJ, Van Rie A. Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries. Brief Bioinform 2020; 22:5917386. [PMID: 33009560 PMCID: PMC8293823 DOI: 10.1093/bib/bbaa246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 11/14/2022] Open
Abstract
Background Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. Methods We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Findings Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. Interpretation By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
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Affiliation(s)
- Emmanuel Rivière
- Corresponding author: Emmanuel Rivière, Faculty of Medicine and Health Sciences, Tuberculosis Omics Research Consortium, Global Health Institute, University of Antwerp Doornstraat 331, Wilrijk 2610, Belgium. Tel.: +32 32658970; E-mail:
| | | | | | | | | | - Gemeda Abebe
- Mycobacteriology Research Center in Jimma, Ethiopia
| | - Peter Heusden
- South African National Bioinformatics Institute (SANBI)
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Joy RA, Thelakkattusserry SK, Vikkath N, Bhaskaran R, Krishnan S, Vasudevan D, Ariyannur PS. Somatic mutation detection efficiency in EGFR: a comparison between high resolution melting analysis and Sanger sequencing. BMC Cancer 2020; 20:902. [PMID: 32962681 PMCID: PMC7510081 DOI: 10.1186/s12885-020-07411-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Background High resolution melting curve analysis is a cost-effective rapid screening method for detection of somatic gene mutation. The performance characteristics of this technique has been explored previously, however, analytical parameters such as limit of detection of mutant allele fraction and total concentration of DNA, have not been addressed. The current study focuses on comparing the mutation detection efficiency of High-Resolution Melt Analysis (HRM) with Sanger Sequencing in somatic mutations of the EGFR gene in non-small cell lung cancer. Methods The minor allele fraction of somatic mutations was titrated against total DNA concentration using Sanger sequencing and HRM to determine the limit of detection. The mutant and wildtype allele fractions were validated by multiplex allele-specific real-time PCR. Somatic mutation detection efficiency, for exons 19 & 21 of the EGFR gene, was compared in 116 formalin fixed paraffin embedded tumor tissues, after screening 275 tumor tissues by Sanger sequencing. Results The limit of detection of minor allele fraction of exon 19 mutation was 1% with sequencing, and 0.25% with HRM, whereas for exon 21 mutation, 0.25% MAF was detected using both methods. Multiplex allele-specific real-time PCR revealed that the wildtype DNA did not impede the amplification of mutant allele in mixed DNA assays. All mutation positive samples detected by Sanger sequencing, were also detected by HRM. About 28% cases in exon 19 and 40% in exon 21, detected as mutated in HRM, were not detected by sequencing. Overall, sensitivity and specificity of HRM were found to be 100 and 67% respectively, and the negative predictive value was 100%, while positive predictive value was 80%. Conclusion The comparative series study suggests that HRM is a modest initial screening test for somatic mutation detection of EGFR, which must further be confirmed by Sanger sequencing. With the modification of annealing temperature of initial PCR, the limit of detection of Sanger sequencing can be improved.
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Affiliation(s)
- Reenu Anne Joy
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | | | - Narendranath Vikkath
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Renjitha Bhaskaran
- Department of Biostatistics, Amrita School of Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Sajitha Krishnan
- Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Damodaran Vasudevan
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India.,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Prasanth S Ariyannur
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India. .,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India.
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