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Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiol 2023; 23:404. [PMID: 38124060 PMCID: PMC10731705 DOI: 10.1186/s12866-023-03147-7] [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: 09/12/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. RESULTS In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models' performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. CONCLUSIONS Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.
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Affiliation(s)
- Alper Yurtseven
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany.
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany.
| | - Sofia Buyanova
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
| | - Amay Ajaykumar Agrawal
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
| | - Olga O Bochkareva
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg, 3400, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Djerassiplatz 1 A, Wien, 1030, Austria
| | - Olga V Kalinina
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken, 66123, Saarland, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, 66123, Saarland, Germany
- Faculty of Medicine, Saarland University, Homburg, 66421, Saarland, Germany
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Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends Microbiol 2021; 29:621-633. [PMID: 33455849 PMCID: PMC8187264 DOI: 10.1016/j.tim.2020.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity within many bacterial species. Awareness of this genetic heterogeneity has corresponded with a greater appreciation of intraspecies variation in virulence. A number of comparative genomic strategies have been developed to link these genotypic and pathogenic differences with the aim of discovering novel virulence factors. Here, we review recent advances in comparative genomic approaches to identify bacterial virulence determinants, with a focus on genome-wide association studies and machine learning.
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Affiliation(s)
- Jonathan P Allen
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA.
| | - Evan Snitkin
- Department of Microbiology and Immunology, Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nathan B Pincus
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine/Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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San JE, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. Front Microbiol 2020; 10:3119. [PMID: 32082269 PMCID: PMC7002396 DOI: 10.3389/fmicb.2019.03119] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
Microbial genome-wide association studies (mGWAS) are a new and exciting research field that is adapting human GWAS methods to understand how variations in microbial genomes affect host or pathogen phenotypes, such as drug resistance, virulence, host specificity and prognosis. Several computational tools and methods have been developed or adapted from human GWAS to facilitate the discovery of novel mutations and structural variations that are associated with the phenotypes of interest. However, no comprehensive, end-to-end, user-friendly tool is currently available. The development of a broadly applicable pipeline presents a real opportunity among computational biologists. Here, (i) we review the prominent and promising tools, (ii) discuss analytical pitfalls and bottlenecks in mGWAS, (iii) provide insights into the selection of appropriate tools, (iv) highlight the gaps that still need to be filled and how users and developers can work together to overcome these bottlenecks. Use of mGWAS research can inform drug repositioning decisions as well as accelerate the discovery and development of more effective vaccines and antimicrobials for pressing infectious diseases of global health significance, such as HIV, TB, influenza, and malaria.
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Affiliation(s)
- James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shakuntala Baichoo
- Department of Digital Technologies, FoICDT, University of Mauritius, Réduit, Mauritius
| | - Aquillah Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yumna Moosa
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Mogaka
- Discipline of Public Health, University of Kwazulu-Natal, Durban, South Africa
| | - Robert Power
- St Edmund Hall, Oxford University, Oxford, United Kingdom
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, United States
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Janies D. Phylogenetic Concepts and Tools Applied to Epidemiologic Investigations of Infectious Diseases. Microbiol Spectr 2019; 7:10.1128/microbiolspec.ame-0006-2018. [PMID: 31325287 PMCID: PMC10956736 DOI: 10.1128/microbiolspec.ame-0006-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Indexed: 01/13/2023] Open
Abstract
In this review, which is a part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, I present an overview of the principles used to classify organisms in the field of phylogenetics, highlight the methods used to infer the interrelationships of organisms, and summarize how these concepts are applied to molecular epidemiologic analyses. I present steps in analyses that come downstream of the assembly of a set of genomes or genes and the production of a multiple-sequence alignment or other matrices of putative orthologs for comparison. I focus on the history of the problem of phylogenetic reconstruction and debates within the field about the most appropriate methods. I illustrate methods that bridge the gap between molecular epidemiology and traditional epidemiology, including phylogenetic character evolution and geographic visualization. Finally, I provide practical advice on how to conduct an example analysis in the appendix. *This article is part of a curated collection.
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Affiliation(s)
- Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
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Handelman SK, Aaronson JM, Seweryn M, Voronkin I, Kwiek JJ, Sadee W, Verducci JS, Janies DA. Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies. Comput Biol Med 2015; 58:1-13. [PMID: 25577610 PMCID: PMC4331246 DOI: 10.1016/j.compbiomed.2014.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Associations between genotype and phenotype provide insight into the evolution of pathogenesis, drug resistance, and the spread of pathogens between hosts. However, common ancestry can lead to apparent associations between biologically unrelated features. The novel method Cladograms with Path to Event (ClaPTE) detects associations between character-pairs (either a pair of mutations or a mutation paired with a phenotype) while adjusting for common ancestry, using phylogenetic trees. METHODS ClaPTE tests for character-pairs changing close together on the phylogenetic tree, consistent with an associated character-pair. ClaPTE is compared to three existing methods (independent contrasts, mixed model, and likelihood ratio) to detect character-pair associations adjusted for common ancestry. Comparisons utilize simulations on gene trees for: HIV Env, HIV promoter, and bacterial DnaJ and GuaB; and case studies for Oseltamavir resistance in Influenza, and for DnaJ and GuaB. Simulated data include both true-positive/associated character-pairs, and true-negative/not-associated character-pairs, used to assess type I (frequency of p-values in true-negatives) and type II (sensitivity to true-positives) error control. RESULTS AND CONCLUSIONS ClaPTE has competitive sensitivity and better type I error control than existing methods. In the Influenza/Oseltamavir case study, ClaPTE reports no new permissive mutations but detects associations between adjacent (in primary sequence) amino acid positions which other methods miss. In the DnaJ and GuaB case study, ClaPTE reports more frequent associations between positions both from the same protein family than between positions from different families, in contrast to other methods. In both case studies, the results from ClaPTE are biologically plausible.
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Affiliation(s)
- Samuel K Handelman
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States; Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States.
| | - Jacob M Aaronson
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Michal Seweryn
- Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States
| | - Igor Voronkin
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Jesse J Kwiek
- Department of Microbial Infection & Immunity and Department of Microbiology, The Ohio State University, 788 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210, United States
| | - Wolfgang Sadee
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Joseph S Verducci
- Department of Statistics, The Ohio State University, 404 Cockins Hall, 1958 Neil Avenue, Columbus, OH 43210-1247, United States
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223-0001, United States
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Wozniak M, Tiuryn J, Wong L. GWAMAR: genome-wide assessment of mutations associated with drug resistance in bacteria. BMC Genomics 2014; 15 Suppl 10:S10. [PMID: 25559874 PMCID: PMC4304204 DOI: 10.1186/1471-2164-15-s10-s10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Development of drug resistance in bacteria causes antibiotic therapies to be less effective and more costly. Moreover, our understanding of the process remains incomplete. One promising approach to improve our understanding of how resistance is being acquired is to use whole-genome comparative approaches for detection of drug resistance-associated mutations. Results We present GWAMAR, a tool we have developed for detecting of drug resistance-associated mutations in bacteria through comparative analysis of whole-genome sequences. The pipeline of GWAMAR comprises several steps. First, for a set of closely related bacterial genomes, it employs eCAMBer to identify homologous gene families. Second, based on multiple alignments of the gene families, it identifies mutations among the strains of interest. Third, it calculates several statistics to identify which mutations are the most associated with drug resistance. Conclusions Based on our analysis of two large datasets retrieved from publicly available data for M. tuberculosis, we identified a set of novel putative drug resistance-associated mutations. As a part of this work, we present also an application of our tool to detect putative compensatory mutations.
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Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics. Mol Phylogenet Evol 2014; 79:279-91. [DOI: 10.1016/j.ympev.2014.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 11/24/2022]
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Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SAFT. Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics 2013; 12:366-80. [PMID: 23625995 PMCID: PMC3743258 DOI: 10.1093/bfgp/elt008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.
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Affiliation(s)
- Bas E Dutilh
- CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.
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Abstract
Background Drug resistance in bacterial pathogens is an increasing problem, which stimulates research. However, our understanding of drug resistance mechanisms remains incomplete. Fortunately, the fast-growing number of fully sequenced bacterial strains now enables us to develop new methods to identify mutations associated with drug resistance. Results We present a new comparative approach to identify genes and mutations that are likely to be associated with drug resistance mechanisms. In order to test the approach, we collected genotype and phenotype data of 100 fully sequenced strains of S. aureus and 10 commonly used drugs. Then, applying the method, we re-discovered the most common genetic determinants of drug resistance and identified some novel putative associations. Conclusions Firstly, the collected data may help other researchers to develop and verify similar techniques. Secondly, the proposed method is successful in identifying drug resistance determinants. Thirdly, the in-silico identified genetic mutations, which are putatively involved in drug resistance mechanisms, may increase our understanding of the drug resistance mechanisms.
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Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SAFT. PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics 2012; 13:170. [PMID: 22559291 PMCID: PMC3366882 DOI: 10.1186/1471-2164-13-170] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 05/04/2012] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances). Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. RESULTS We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/) that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene) selection is based. Preprocessed data is used in feature (e.g., gene) selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value) to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. CONCLUSIONS PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing), gene expression (determined by e.g.: microarrays or RNA-seq), or metabolite abundance (determined by e.g.: GC-MS).
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Affiliation(s)
- Jumamurat R Bayjanov
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Douwe Molenaar
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, Ede 6710 BA, The Netherlands
- Systems Bioinformatics IBIVU, Free University of Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Vesela Tzeneva
- TI Food and Nutrition, P.O. Box 557, Wageningen 6700 AN, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, Ede 6710 BA, The Netherlands
| | - Roland J Siezen
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- TI Food and Nutrition, P.O. Box 557, Wageningen 6700 AN, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, Ede 6710 BA, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- TI Food and Nutrition, P.O. Box 557, Wageningen 6700 AN, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, Ede 6710 BA, The Netherlands
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Nakajima K, Tanaka Y. Exclusion of Kif1c as a candidate gene for anthrax toxin susceptibility. Microb Pathog 2010; 48:188-90. [PMID: 20188815 DOI: 10.1016/j.micpath.2010.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
Abstract
Different strains of mice possess varying degrees of susceptibility to anthrax lethal toxin (LT). Previous studies have suggested a responsible locus Ltxs1 that contains 10 or more known genes, but functional relevance has been reported for two genes, Kif1c and Nalp1b. In this study, we attempted to determine the involvement of Kif1c in anthrax susceptibility using Kif1c knockout mice. We established Kif1c knockout mice with LT-sensitive 129/Sv-derived embryonic stem cells followed by 13 backcrosses with LT-resistant C57BL/6J mice (B6) to be congenic. These knockout mice and their primary macrophages showed significantly higher sensitivity to LT than wild-type B6. However, when we replaced the remaining 129/Sv genome adjacent to the targeted Kif1c locus with the B6 genome, this sensitivity was lost. This suggested that the sensitivity to LT in the originally established Kif1c knockout mice was not due to the loss of the Kif1c gene, but was because of the presence of the 129/Sv-derived genes adjacent to the disrupted Kif1c locus. Thus, Kif1c was excluded as a candidate anthrax susceptibility gene.
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Affiliation(s)
- Kazuo Nakajima
- Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, Hongo, Tokyo 113-0033, Japan.
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Hill AW, Guralnick RP, Wilson MJC, Habib F, Janies D. Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. INFECTION GENETICS AND EVOLUTION 2008; 9:169-78. [PMID: 19022400 DOI: 10.1016/j.meegid.2008.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 10/12/2008] [Accepted: 10/13/2008] [Indexed: 12/15/2022]
Abstract
Some predict that influenza A H5N1 will be the cause of a pandemic among humans. In preparation for such an event, many governments and organizations have stockpiled antiviral drugs such as oseltamivir (Tamiflu). However, it is known that multiple lineages of H5N1 are already resistant to another class of drugs, adamantane derivatives, and a few lineages are resistant to oseltamivir. What is less well understood is the evolutionary history of the mutations that confer drug resistance in the H5N1 population. In order to address this gap, we conducted phylogenetic analyses of 676 genomic sequences of H5N1 and used the resulting hypotheses as a basis for asking 3 molecular evolutionary questions: (1) Have drug-resistant genotypes arisen in distinct lineages of H5N1 through point mutation or through reassortment? (2) Is there evidence for positive selection on the codons that lead to drug resistance? (3) Is there evidence for covariation between positions in the genome that confer resistance to drugs and other positions, unrelated to drug resistance, that may be under selection for other phenotypes? We also examine how drug-resistant lineages proliferate across the landscape by projecting or phylogenetic analysis onto a virtual globe. Our results for H5N1 show that in most cases drug resistance has arisen by independent point mutations rather than reassortment or covariation. Furthermore, we found that some codons that mediate resistance to adamantane derivatives are under positive selection, but did not find positive selection on codons that mediate resistance to oseltamivir. Together, our phylogenetic methods, molecular evolutionary analyses, and geographic visualization provide a framework for analysis of globally distributed genomic data that can be used to monitor the evolution of drug resistance.
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Affiliation(s)
- Andrew W Hill
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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Leiman DA, Lorenzi NM, Wyatt JC, Doney ASF, Rosenbloom ST. US and Scottish health professionals' attitudes toward DNA biobanking. J Am Med Inform Assoc 2008; 15:357-62. [PMID: 18308988 DOI: 10.1197/jamia.m2571] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The authors define a DNA biobank as a repository of genetic information correlated with patient medical records. DNA biobanks may assist in the research and identification of genetic factors influencing disease and drug interactions, but may raise ethical issues. How healthcare providers perceive DNA biobanks is unknown. OBJECTIVES To determine how useful healthcare professionals believe DNA biobanks will be and whether these attitudes differ between private and socialized healthcare systems. DESIGN The authors surveyed 200 healthcare professionals, including research and non-research focused doctors, nurses and other staff from medical centers and independent practice in both the United States and Scotland. The survey included fifteen items evaluated for general receptiveness toward biobanks, presumed usefulness of biobanks and perceived attitudes in recruiting patients for a biobank. MEASUREMENTS A total of 81 (45%) of 179 eligible participants responded: 41 from the U.S. and 40 from Scotland. Of these respondents, most (70%) were from academic centers. RESULTS Results indicate that there is a broadly favorable attitude in both locations toward the creation of a DNA biobank (83%) and its perceived benefit (75%). This enthusiasm is tempered in Scotland when respondents evaluated their comfort in consenting patients for entry into a biobank; 16 of 40 respondents (40%) were uncomfortable doing so, representing a significant difference from those in the U.S. (p=0.001). CONCLUSIONS Despite systematic differences in healthcare practice between the U.S. and Scotland, health care professionals in both nations believe DNA biobanks will be useful in curing disease. This finding appears to support further development of such a research tool.
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