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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: 43] [Impact Index Per Article: 10.8] [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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102
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Terret-Welter Z, Bonnet G, Moury B, Gallois JL. Analysis of tomato spotted wilt virus RNA-dependent RNA polymerase adaptative evolution and constrained domains using homology protein structure modelling. J Gen Virol 2020; 101:334-346. [PMID: 31958051 DOI: 10.1099/jgv.0.001380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tomato spotted wilt virus (TSWV; genus Orthotospovirus, family Tospoviridae) has a huge impact on a large range of plants worldwide. In this study, we determined the sequence of the large (L) RNA segment that encodes the RNA-dependent RNA polymerase (RdRp) from a TSWV isolate (LYE51) collected in the south of France. Analysis of the phylogenetic relationships of TSWV-LYE51 with other TSWV isolates shows that it is closely related to other European isolates. A 3D model of TSWV-LYE51 RdRp was built by homology with the RdRp structure of the La Crosse virus (genus Orthobunyavirus, family Peribunyaviridae). Finally, an analysis of positive and negative selection was carried out on 30 TSWV full-length RNA L sequences and compared with the phylogeny and the protein structure data. We showed that the seven codons that are under positive selection are distributed all along the RdRp gene. By contrast, the codons associated with negative selection are especially concentrated in three highly constrained domains: the endonuclease in charge of the cap-snatching mechanism, the thumb domain and the mid domain. Those three domains could constitute good candidates to look for host targets on which genetic resistance by loss of susceptibility could be developed.
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Affiliation(s)
- Zoé Terret-Welter
- Syngeta Seeds SAS, 346 Route des Pasquiers - F84260 Sarrians, France
- GAFL, INRA, Montfavet, France
| | - Grégori Bonnet
- Syngeta Seeds SAS, 346 Route des Pasquiers - F84260 Sarrians, France
| | - Benoit Moury
- INRA, UR407 Pathologie Végétale, 84140, Montfavet, France
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103
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Wang S, Zhou Y, Zhao B, Ou X, Xia H, Zheng Y, Song Y, Cheng Q, Wang X, Zhao Y. Characteristics of compensatory mutations in the rpoC gene and their association with compensated transmission of Mycobacterium tuberculosis. Front Med 2020; 14:51-59. [PMID: 31938981 DOI: 10.1007/s11684-019-0720-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/07/2019] [Indexed: 11/26/2022]
Abstract
The aim of this study was to characterize rpoC gene mutations in Mycobacterium tuberculosis (MTB) and investigate the factors associated with rpoC mutations and the relation between rpoC mutations and tuberculosis (TB) transmission. A total of 245 MTB clinical isolates from patients with TB in six provinces and two municipalities in China were characterized based on gene mutations through DNA sequencing of rpoC and rpoB genes, phenotyping via standard drug susceptibility testing, and genotypic profiling by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. Approximately 36.4% of the rifampin-resistant isolates harbored nonsynonymous mutations in the rpoC gene. Twenty-nine nonsynonymous single mutations and three double mutations were identified. The rpoC mutations at locus 483 (11.3%) were predominant, and the mutations at V483G, W484G, I491V, L516P, L566R, N698K, and A788E accounted for 54.5% of the total detected mutations. Fifteen new mutations in the rpoC gene were identified. Rifampin resistance and rpoB mutations at locus 531 were significantly associated with rpoC mutations. MIRU-VNTR genotype results indicated that 18.4% of the studied isolates were clustered, and the rpoC mutations were not significantly associated with MIRU-VNTR clusters. A large proportion of rpoC mutation was observed in the rifampicin-resistant MTB isolates. However, the findings of this study do not support the association of rpoC mutation with compensated transmissibility.
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Affiliation(s)
- Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Zheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuanyuan Song
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qian Cheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinyang Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Microbiology, Basic Medicine College, Harbin Medical University, Harbin, 150081, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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104
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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105
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Vila Nova M, Durimel K, La K, Felten A, Bessières P, Mistou MY, Mariadassou M, Radomski N. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics 2019; 20:814. [PMID: 31694533 PMCID: PMC6836353 DOI: 10.1186/s12864-019-6188-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv). RESULTS Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively. CONCLUSIONS Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.
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Affiliation(s)
- Meryl Vila Nova
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Kévin Durimel
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Kévin La
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Arnaud Felten
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Philippe Bessières
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel-Yves Mistou
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Mahendra Mariadassou
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Radomski
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France.
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106
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Minias A, Minias P, Czubat B, Dziadek J. Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis. Genome Biol Evol 2019; 10:2326-2337. [PMID: 30060031 PMCID: PMC6363050 DOI: 10.1093/gbe/evy153] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection University of Łódź, Łódź, Poland
| | - Bożena Czubat
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland.,Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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107
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Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam. Sci Rep 2019; 9:15354. [PMID: 31653940 PMCID: PMC6814805 DOI: 10.1038/s41598-019-51812-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a serious global problem, and pathogen factors involved in the transmission of isoniazid (INH)-resistant TB have not been fully investigated. We performed whole genome sequencing of 332 clinical Mycobacterium tuberculosis (Mtb) isolates collected from patients newly diagnosed with smear-positive pulmonary TB in Hanoi, Vietnam. Using a bacterial genome-wide approach based on linear mixed models, we investigated the associations between 31-bp k-mers and clustered strains harboring katG-S315T, a major INH-resistance mutation in the present cohort and in the second panel previously published in South Africa. Five statistically significant genes, namely, PPE18/19, gid, emrB, Rv1588c, and pncA, were shared by the two panels. We further identified variants of the genes responsible for these k-mers, which are relevant to the spread of INH-resistant strains. Phylogenetic convergence test showed that variants relevant to PPE46/47-like chimeric genes were significantly associated with the same phenotype in Hanoi. The associations were further confirmed after adjustment for the confounders. These findings suggest that genomic variations of the pathogen facilitate the expansion of INH-resistance TB, at least in part, and our study provides a new insight into the mechanisms by which drug-resistant Mtb maintains fitness and spreads in Asia and Africa.
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108
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Hicks AL, Wheeler N, Sánchez-Busó L, Rakeman JL, Harris SR, Grad YH. Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. PLoS Comput Biol 2019; 15:e1007349. [PMID: 31479500 PMCID: PMC6743791 DOI: 10.1371/journal.pcbi.1007349] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/13/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Prediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics. However, there has been no systematic evaluation of factors that may influence performance of such models, how they might apply to and vary across clinical populations, and what the implications might be in the clinical setting. Here, we performed a meta-analysis of seven large Neisseria gonorrhoeae datasets, as well as Klebsiella pneumoniae and Acinetobacter baumannii datasets, with whole genome sequence data and antibiotic susceptibility phenotypes using set covering machine classification, random forest classification, and random forest regression models to predict resistance phenotypes from genotype. We demonstrate how model performance varies by drug, dataset, resistance metric, and species, reflecting the complexities of generating clinically relevant conclusions from machine learning-derived models. Our findings underscore the importance of incorporating relevant biological and epidemiological knowledge into model design and assessment and suggest that doing so can inform tailored modeling for individual drugs, pathogens, and clinical populations. We further suggest that continued comprehensive sampling and incorporation of up-to-date whole genome sequence data, resistance phenotypes, and treatment outcome data into model training will be crucial to the clinical utility and sustainability of machine learning-based molecular diagnostics.
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Affiliation(s)
- Allison L. Hicks
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
| | - Nicole Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer L. Rakeman
- Public Health Laboratory, Division of Disease Control, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Simon R. Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
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109
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Chiner-Oms Á, Comas I. Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2019; 72:10-15. [DOI: 10.1016/j.meegid.2019.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023]
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110
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Kordes A, Preusse M, Willger SD, Braubach P, Jonigk D, Haverich A, Warnecke G, Häussler S. Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. Nat Commun 2019; 10:3397. [PMID: 31363089 PMCID: PMC6667473 DOI: 10.1038/s41467-019-11414-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Previous studies have demonstrated substantial genetic diversification of Pseudomonas aeruginosa across sub-compartments in cystic fibrosis (CF) lungs. Here, we isolate P. aeruginosa from five different sampling areas in the upper and lower airways of an explanted CF lung, analyze ex vivo transcriptional profiles by RNA-seq, and use colony re-sequencing and deep population sequencing to determine the genetic diversity within and across the various sub-compartments. We find that, despite genetic variation, the ex vivo transcriptional profiles of P. aeruginosa populations inhabiting different regions of the CF lung are similar. Although we cannot estimate the extent to which the transcriptional response recorded here actually reflects the in vivo transcriptomes, our results indicate that there may be a common in vivo transcriptional profile in the CF lung environment.
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Affiliation(s)
- Adrian Kordes
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Matthias Preusse
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Sven D Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School, Hannover, 30625, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, 30625, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
| | - Axel Haverich
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
- Department of Cardiothoracic, Transplant and Vascular Surgery, Hannover Medical School, Hannover, 30625, Germany
| | - Gregor Warnecke
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
- Department of Cardiothoracic, Transplant and Vascular Surgery, Hannover Medical School, Hannover, 30625, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany.
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany.
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111
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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112
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Sergeev RS, Kavaliou IS, Sataneuski UV, Gabrielian A, Rosenthal A, Tartakovsky M, Tuzikov AV. Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus: Machine-Learning Approach. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1398-1408. [PMID: 28678713 DOI: 10.1109/tcbb.2017.2720669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Emergence of drug-resistant microorganisms has been recognized as a serious threat to public health worldwide. This problem is extensively discussed in the context of tuberculosis treatment. Alterations in pathogen genomes are among the main mechanisms by which microorganisms exhibit drug resistance. Analysis of 144 M. tuberculosis strains of different phenotypes including drug susceptible, MDR, and XDR isolated in Belarus was fulfilled in this paper. A wide range of machine learning methods that can discover SNPs related to drug-resistance in the whole bacteria genomes was investigated. Besides single-SNP testing approaches, methods that allow detecting joint effects from interacting SNPs were considered. We proposed a framework for automated selection of the best performing statistical model in terms of recall, precision, and accuracy to identify drug resistance-associated mutations. Analysis of whole-genome sequences often leads to situations where the number of treated features exceeds the number of available observations. For this reason, special attention is paid to fair evaluation of the model prediction quality and minimizing the risk of overfitting while estimating the underlying parameters. Results of our experiments aimed at identifying top-scoring resistance mutations to the major first-line and second-line anti-TB drugs are presented.
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113
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Yang Y, Niehaus KE, Walker TM, Iqbal Z, Walker AS, Wilson DJ, Peto TEA, Crook DW, Smith EG, Zhu T, Clifton DA. Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data. Bioinformatics 2019; 34:1666-1671. [PMID: 29240876 PMCID: PMC5946815 DOI: 10.1093/bioinformatics/btx801] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/10/2017] [Indexed: 01/07/2023] Open
Abstract
Motivation Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence of any well-studied single nucleotide polymorphisms is sufficient to cause resistance, which yields low sensitivity for resistance classification. Summary Given the availability of DNA sequencing data from MTB, we developed machine learning models for a cohort of 1839 UK bacterial isolates to classify MTB resistance against eight anti-TB drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, ciprofloxacin, moxifloxacin, ofloxacin, streptomycin) and to classify multi-drug resistance. Results Compared to previous rules-based approach, the sensitivities from the best-performing models increased by 2-4% for isoniazid, rifampicin and ethambutol to 97% (P < 0.01), respectively; for ciprofloxacin and multi-drug resistant TB, they increased to 96%. For moxifloxacin and ofloxacin, sensitivities increased by 12 and 15% from 83 and 81% based on existing known resistance alleles to 95% and 96% (P < 0.01), respectively. Particularly, our models improved sensitivities compared to the previous rules-based approach by 15 and 24% to 84 and 87% for pyrazinamide and streptomycin (P < 0.01), respectively. The best-performing models increase the area-under-the-ROC curve by 10% for pyrazinamide and streptomycin (P < 0.01), and 4–8% for other drugs (P < 0.01). Availability and implementation The details of source code are provided at http://www.robots.ox.ac.uk/~davidc/code.php. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Yang
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
| | - Katherine E Niehaus
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
| | - Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Zamin Iqbal
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK.,National Infection Service, Public Health England, Colindale, London, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK
| | | | - Tingting Zhu
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
| | - David A Clifton
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
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114
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Liao J, Orsi RH, Carroll LM, Kovac J, Ou H, Zhang H, Wiedmann M. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol Biol 2019; 19:132. [PMID: 31226931 PMCID: PMC6588947 DOI: 10.1186/s12862-019-1457-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 06/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium). Results AMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins. Conclusions Our data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica. Electronic supplementary material The online version of this article (10.1186/s12862-019-1457-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.,Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Renato Hohl Orsi
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongyu Ou
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hailong Zhang
- Department of Computer Science & Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Martin Wiedmann
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.
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115
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Palmer AC, Chait R, Kishony R. Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance. Mol Biol Evol 2019; 35:2669-2684. [PMID: 30169679 PMCID: PMC6231494 DOI: 10.1093/molbev/msy163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness–expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.
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Affiliation(s)
- Adam C Palmer
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Departments of Biology and Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
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116
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Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
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Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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117
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Sackton TB, Clark N. Convergent evolution in the genomics era: new insights and directions. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190102. [PMID: 31154976 DOI: 10.1098/rstb.2019.0102] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
| | - Nathan Clark
- 2 Computational and Systems Biology, University of Pittsburgh , PA , USA
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118
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Chiner-Oms Á, Sánchez-Busó L, Corander J, Gagneux S, Harris SR, Young D, González-Candelas F, Comas I. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. SCIENCE ADVANCES 2019; 5:eaaw3307. [PMID: 31448322 PMCID: PMC6691555 DOI: 10.1126/sciadv.aaw3307] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/10/2019] [Indexed: 06/10/2023]
Abstract
Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.
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Affiliation(s)
- Á. Chiner-Oms
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
| | - L. Sánchez-Busó
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - J. Corander
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
- Helsinki Institute of Information Technology (HIIT), Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - S. Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - S. R. Harris
- Microbiotica, BioData Innovation Centre, Wellcome Genome Campus, Cambridge CB10 1DR, UK
| | - D. Young
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - F. González-Candelas
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - I. Comas
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
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119
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GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nat Commun 2019; 10:2128. [PMID: 31086182 PMCID: PMC6513847 DOI: 10.1038/s41467-019-10110-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/18/2019] [Indexed: 01/28/2023] Open
Abstract
Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.
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120
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Whole-Genome Sequencing in Relation to Resistance of Mycobacterium Tuberculosis. ACTA MEDICA MARTINIANA 2019. [DOI: 10.2478/acm-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract
Tuberculosis, a disease caused by Mycobacterium tuberculosis, represents one of the deadliest infections worldwide. The incidence of resistant forms is increasing year by year; therefore, it is necessary to involve new methods for rapid diagnostics and treatment. One of the possible solutions is the use of whole-genome sequencing (WGS).
The WGS provides an identification of complete genome of the microorganism, including all genes responsible for resistance, in comparison with other genotypic methods (eg. Xpert MTB / RIF or Hain line-probes) that are capable to detect only basic genes. WGS data are available in 1-9 days and several online software tools (TBProfiler, CASTB, Mykrobe PredictorTB) are used for their interpretation and analysis, compared to 3-8 weeks in the case of classic phenotypic evaluation.
Furthermore, WGS predicts resistance to the first-line antituberculotics with a sensitivity of 85-100% and a specificity of 85-100%.
This review elucidates the importance and summarizes the current knowledge about the possible use of WGS in diagnosis and treatment of resistant forms of tuberculosis elucidates.
WGS of M. tuberculosis brings new possibilities for rapid and accurate diagnostics of resistant forms of tuberculosis. Introducing WGS into routine practice can help to reduce the spread of resistant forms of tuberculosis as well as to increase the success rate of the treatment, especially through an appropriate combination of antituberculotics ATs. Introduction of WGS into routine diagnostics can, in spite of the financial difficulty, significantly improve patient care.
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121
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Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
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122
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Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep 2019; 9:5602. [PMID: 30944370 PMCID: PMC6447560 DOI: 10.1038/s41598-019-41967-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/20/2019] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.
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Affiliation(s)
- Avika Dixit
- Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | - Zibiao Zhang
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Leonid Lecca
- Harvard Medical School, Boston, MA, USA
- Socios En Salud, Lima, Peru
| | | | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maha R Farhat
- Harvard Medical School, Boston, MA, USA
- Massachussetts General Hospital, Boston, MA, USA
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123
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Oppong YEA, Phelan J, Perdigão J, Machado D, Miranda A, Portugal I, Viveiros M, Clark TG, Hibberd ML. Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance. BMC Genomics 2019; 20:252. [PMID: 30922221 PMCID: PMC6440112 DOI: 10.1186/s12864-019-5615-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
Background Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to elucidate the genetic basis of anti-microbial drug resistance and gain a more detailed understanding of Mtb genome evolution in a context of widespread antimicrobial therapy. Population structure within the Mtb complex, due to clonal expansion, lack of lateral gene transfer and low levels of recombination between lineages, may be reducing statistical power to detect drug resistance associated variants. Results To investigate the effect of lineage-specific effects on the identification of drug resistance associations, we applied genome-wide association study (GWAS) and convergence-based (PhyC) methods to multiple drug resistance phenotypes of a global dataset of Mtb lineages 2 and 4, using both lineage-wise and combined approaches. We identify both well-established drug resistance variants and novel associations; uniquely identifying associations for both lineage-specific and -combined GWAS analyses. We report 17 potential novel associations between antimicrobial resistance phenotypes and Mtb genomic variants. Conclusions For GWAS, both lineage-specific and -combined analyses are useful, whereas PhyC may perform better in contexts of greater diversity. Unique associations with XDR in lineage-specific analyses provide evidence of diverging evolutionary trajectories between lineages 2 and 4 in response to antimicrobial drug therapy. Electronic supplementary material The online version of this article (10.1186/s12864-019-5615-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaa E A Oppong
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Jody Phelan
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - João Perdigão
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - Isabel Portugal
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Taane G Clark
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Faculty of Epidemiology and Population Health, LSHTM, London, UK
| | - Martin L Hibberd
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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124
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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125
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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden. Sci Rep 2019; 9:4931. [PMID: 30894568 PMCID: PMC6426893 DOI: 10.1038/s41598-019-39971-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.
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Thomas AK, Preetha S, Omanakuttan A, Vidyullata L, Ashokan A, Rajachandran V, Chattopadhyay S. Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp. Sci Rep 2019; 9:3252. [PMID: 30824790 PMCID: PMC6397287 DOI: 10.1038/s41598-019-39810-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/25/2019] [Indexed: 12/17/2022] Open
Abstract
Shigella spp., emerging from multiple origins of Escherichia coli, poses a significant health threat as a causative agent of bacillary dysentery. While multiple serotypes of four different species have evolved via independent lineages, Shigella spp. are designated as a single pathotype, primarily because of their common mode of pathogenesis. Convergent horizontal transfer events have so far been attributed to the commonalities in the evolution of virulence across diverse lineages. However, the role of mutational convergence in such parallel evolution is not yet well understood. Here we have carried out a genome-wide analysis of Shigella strains from all four species to detect the core genes (i.e. the ones present in all analyzed strains) acquiring convergent mutations of evolutionarily recent origin. Simulation studies show non-neutral accumulation of these convergent mutations across species, suggesting their adaptive role in the evolution of Shigella virulence. S. dysenteriae strain 197, representing highly virulent type 1 (Sd1) clone, carries excessively high number of core genes with recent convergent mutations compared to other analyzed strains. We propose that this high frequency of adaptive convergence in S. dysenteriae strain 197 could be linked to recent re-emergence of the Sd1 clone and its increased resistance to antimicrobials.
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Affiliation(s)
- Achsah K Thomas
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Sruthy Preetha
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Anjana Omanakuttan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Lakkaraju Vidyullata
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Anjaly Ashokan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Vyshakh Rajachandran
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Sujay Chattopadhyay
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India.
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127
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Omar SV, Joseph L, Said HM, Ismail F, Ismail N, Gwala TL, Ismail NA. Whole genome sequencing for drug resistance determination in Mycobacterium tuberculosis. Afr J Lab Med 2019; 8:801. [PMID: 30863717 PMCID: PMC6407317 DOI: 10.4102/ajlm.v8i1.801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/28/2018] [Indexed: 11/03/2022] Open
Abstract
South Africa remains challenged with a high tuberculosis burden accompanied by an increase in drug resistant cases. We assessed the use of the Illumina MiSeq, a next-generation sequencing platform for whole genome sequencing, followed by bioinformatic analysis using a commercial software package to determine resistance to selected drugs used for Mycobacterium tuberculosis treatment in our setting. Whole genome sequencing shows potential as a diagnostic platform for the detection of drug resistance in Mycobacterium tuberculosis with the provision of information for several drugs simultaneously.
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Affiliation(s)
- Shaheed V Omar
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lavania Joseph
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Halima M Said
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Department of Medical Microbiology, University of the Free State, Bloemfontein, South Africa
| | - Farzana Ismail
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nabila Ismail
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Thabisile L Gwala
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nazir A Ismail
- Centre for Tuberculosis, World Health Organization TB Supranational Reference Laboratory Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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128
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Crispell J, Balaz D, Gordon SV. HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny. Microb Genom 2019; 5:e000245. [PMID: 30663960 PMCID: PMC6412054 DOI: 10.1099/mgen.0.000245] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/26/2018] [Indexed: 01/10/2023] Open
Abstract
A homoplasy is a nucleotide identity resulting from a process other than inheritance from a common ancestor. Importantly, by distorting the ancestral relationships between nucleotide sequences, homoplasies can change the structure of the phylogeny. Homoplasies can emerge naturally, especially under high selection pressures and/or high mutation rates, or be created during the generation and processing of sequencing data. Identification of homoplasies is critical, both to understand their influence on the analyses of phylogenetic data and to allow an investigation into how they arose. Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and Java, HomoplasyFinder is shown to be able to automatically, and quickly, identify any homoplasies present in simulated and real phylogenetic data. HomoplasyFinder can easily be incorporated into existing analysis pipelines, either within or outside of R, allowing the user to quickly identify homoplasies to inform downstream analyses and interpretation.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, College of Health and Agricultural Sciences, University College Dublin, Republic of Ireland
| | - Daniel Balaz
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland
| | - Stephen Vincent Gordon
- School of Veterinary Medicine, College of Health and Agricultural Sciences, University College Dublin, Republic of Ireland
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129
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Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL. Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. Emerg Microbes Infect 2019; 8:109-118. [PMID: 30866765 PMCID: PMC6334779 DOI: 10.1080/22221751.2018.1561158] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 01/08/2023]
Abstract
Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium tuberculosis (causative agent of tuberculosis), Mycobacterium leprae (causative agent of leprosy) and Mycobacterium abscessus (causative agent of chronic pulmonary infections) pose concern to global public health. Although antibiotics have been successfully developed to combat each of these, the emergence of drug-resistant strains is an increasing challenge for treatment and drug discovery. Here we describe the impact of the rapid expansion of genome sequencing and genome/pathway annotations that have greatly improved the progress of structure-guided drug discovery. We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. The opportunities and challenges for the design of drugs for M. tuberculosis, M. leprae and M. abscessus to combat resistance are discussed.
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Affiliation(s)
| | | | | | | | - Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marcin J. Skwark
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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130
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Evolution of Rifampin Resistance in Escherichia coli and Mycobacterium smegmatis Due to Substandard Drugs. Antimicrob Agents Chemother 2018; 63:AAC.01243-18. [PMID: 30397062 DOI: 10.1128/aac.01243-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/31/2018] [Indexed: 01/25/2023] Open
Abstract
Poor-quality medicines undermine the treatment of infectious diseases, such as tuberculosis, which require months of treatment with rifampin and other drugs. Rifampin resistance is a critical concern for tuberculosis treatment. While subtherapeutic doses of medicine are known to select for antibiotic resistance, the effect of drug degradation products on the evolution of resistance is unknown. Here, we demonstrate that substandard drugs that contain degraded active pharmaceutical ingredients select for gene alterations that confer resistance to standard drugs. We generated drug-resistant Escherichia coli and Mycobacterium smegmatis strains by serially culturing bacteria in the presence of the rifampin degradation product rifampin quinone. We conducted Sanger sequencing to identify mutations in rifampin-resistant populations. Strains resistant to rifampin quinone developed cross-resistance to the standard drug rifampin, with some populations showing no growth inhibition at maximum concentrations of rifampin. Sequencing of the rifampin quinone-treated strains indicated that they acquired mutations in the DNA-dependent RNA polymerase B subunit. These mutations were localized in the rifampin resistance-determining region (RRDR), consistent with other reports of rifampin-resistant E. coli and mycobacteria. Rifampin quinone-treated mycobacteria also had cross-resistance to other rifamycin class drugs, including rifabutin and rifapentine. Our results strongly suggest that substandard drugs not only hinder individual patient outcomes but also restrict future treatment options by actively contributing to the development of resistance to standard medicines.
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131
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans. PLoS Pathog 2018; 14:e1007453. [PMID: 30532201 PMCID: PMC6300292 DOI: 10.1371/journal.ppat.1007453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/19/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions. Cystic fibrosis (CF) is the most common lethal genetic disorder affecting individuals of European descent. Most CF patients die at a young age due to chronic lung infections. Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex (BCC), which are strongly associated with poor clinical prognosis. This study examines how the most prevalent BCC species among CF patients, B. multivorans, evolves within a single CF patient by studying the first B. multivorans isolate recovered from the patient, one hundred isolates recovered over a one year period during the chronic infection phase, and an additional ten isolates recovered after the reinfection of the transplanted lungs. We found that B. multivorans diversify phenotypically and genetically within the CF lung over the course of the infection, and evolves into a complex population during the chronic infection phase. We found that isolates collected from the post-transplant reinfection were more closely related to descendants of the original isolate rather than those recovered in the chronic infection. We identify genetic variants statistically associated with resistance to the antibiotics, and showed that some of these variants were found in regions that show patterns of recombination (genetic exchange) between strains. We also found that genes which were mutated multiple times during overall infection were more likely to be found in regions showing signals consistent with recombination. The presence of multiple independent mutations in a gene is a very strong signal that the gene helps bacteria adapt to their environment. Overall, this study provides insight into how pathogens adapt to the host during long-term infections, specific genes associated with antibiotic resistance, and the origin of new and recurrent infections.
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Affiliation(s)
- Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D. Elizabeth Tullis
- Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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132
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Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q. China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nat Ecol Evol 2018; 2:1982-1992. [PMID: 30397300 PMCID: PMC6295914 DOI: 10.1038/s41559-018-0680-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022]
Abstract
A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China-the country with the third highest tuberculosis burden-we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population.
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Affiliation(s)
- Qingyun Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Aijing Ma
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lanhai Wei
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Pang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Beibei Wu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tao Luo
- West China School of Basic Medical Sciences and Forensic Medicines, Sichuan University, Chengdu, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Mingyu Gan
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Tianyu Zuo
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mei Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, CSIC and CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- Shenzhen Center for Chronic Disease Control, Shenzhen, China.
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133
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Jaillard M, Lima L, Tournoud M, Mahé P, van Belkum A, Lacroix V, Jacob L. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet 2018; 14:e1007758. [PMID: 30419019 PMCID: PMC6258240 DOI: 10.1371/journal.pgen.1007758] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/26/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular, it does not require prior annotation or reference genomes. It produces subgraphs representing phenotype-associated genetic variants such as local polymorphisms and mobile genetic elements (MGE). It offers a graphical framework which helps interpret GWAS results. Importantly it is also computationally efficient-experiments took one hour and a half on average. We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis, and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa-along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature. An open-source tool implementing DBGWAS is available at https://gitlab.com/leoisl/dbgwas.
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Affiliation(s)
- Magali Jaillard
- bioMérieux, Marcy l’Étoile, France
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
| | - Leandro Lima
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | | | | | | | - Vincent Lacroix
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Laurent Jacob
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
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Wang ZQ, Meng FZ, Zhang MM, Yin LF, Yin WX, Lin Y, Hsiang T, Peng YL, Wang ZH, Luo CX. A Putative Zn 2Cys 6 Transcription Factor Is Associated With Isoprothiolane Resistance in Magnaporthe oryzae. Front Microbiol 2018; 9:2608. [PMID: 30429837 PMCID: PMC6220061 DOI: 10.3389/fmicb.2018.02608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022] Open
Abstract
Isoprothiolane (IPT), a systemic fungicide, has been applied to control rice blast since the 1970s. Although resistance to IPT has been observed, the mechanism of resistance still has not been fully elucidated. In this study, nucleotide polymorphisms were detected between two IPT-resistant mutants generated in the lab, and their parental wild type isolates using a whole-genome sequencing approach. In the genomes of the two resistant mutants, single point mutations were identified in a gene encoding a Zn2Cys6 transcription factor-like protein. Notably, either knocking out the gene or replacing the wild type allele with the mutant allele (R343W) in a wild type isolate resulted in resistance to IPT, indicating that the gene is associated with IPT resistance, and thus was designated as MoIRR (Magnaporthe oryzae isoprothiolane resistance related). Along with point mutations R343W in mutant 1a_mut, and R345C in 1c_mut, a 16 bp insertion in 6c_mut was also located in the Fungal_TF_MHR domain of MoIRR, revealing that this domain may be the core element for IPT resistance. In addition, IPT-resistant mutants and transformants showed cross-resistance with iprobenfos (IBP), which was consistent with previous observations. These results indicated that MoIRR is strongly connected to resistance to choline biosynthesis inhibitor (CBI), and further work should focus on investigating downstream effects of MoIRR.
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Affiliation(s)
- Zuo-Qian Wang
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fan-Zhu Meng
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming-Ming Zhang
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang-Fen Yin
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wei-Xiao Yin
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - You-Liang Peng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zong-Hua Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao-Xi Luo
- Department of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
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Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun 2018; 9:4306. [PMID: 30333483 PMCID: PMC6193043 DOI: 10.1038/s41467-018-06634-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens.
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Affiliation(s)
- Erol S Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Edward Catoiu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - James T Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas Dillon
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - David Heckmann
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amitesh Anand
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Laurence Yang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA. .,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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136
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Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JOH, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O’Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. SCIENCE ADVANCES 2018; 4:eaat5869. [PMID: 30345355 PMCID: PMC6192687 DOI: 10.1126/sciadv.aat5869] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread of L4 tuberculosis (TB). Markedly, in the age of antibiotics, mutations conferring antimicrobial resistance overwhelmingly emerged locally (at the level of nations), with minimal cross-border transmission of resistance. The latter finding was found to reflect the relatively recent emergence of these mutations, as a similar degree of local restriction was observed for susceptible variants emerging on comparable time scales. The restricted international transmission of drug-resistant TB suggests that containment efforts at the level of individual countries could be successful.
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Affiliation(s)
- Ola B. Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Caitlin S. Pepperell
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Avenida Brasil 4365, C.P. 926, Manguinhos 21040-360, Rio de Janeiro, Brazil
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College London, W2 1NY, London, UK
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Nadia Debech
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Jon Bohlin
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Kristian Alfsnes
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - John O.-H. Pettersson
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
- Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
| | - Ingerid Kirkeleite
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Fatima Fandinho
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Marcia Aparecida da Silva
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Joao Perdigao
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Taane Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Maxine Caws
- Liverpool School of Tropical medicine, Department of Clinical Sciences, Liverpool, UK
- Birat-Nepal Medical Trust, Lazimpat, Kathmandu, Nepal
| | - Sarah Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler S. Brown
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dick van Soolingen
- Center for Infectious Disease Research, Diagnostics and Perinatal Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, Netherlands
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn E. Holt
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Edward J. Feil
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
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137
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Nguyen QH, Contamin L, Nguyen TVA, Bañuls A. Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis. Evol Appl 2018; 11:1498-1511. [PMID: 30344622 PMCID: PMC6183457 DOI: 10.1111/eva.12654] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 01/01/2023] Open
Abstract
At present, the successful transmission of drug-resistant Mycobacterium tuberculosis, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, in human populations, threatens tuberculosis control worldwide. Differently from many other bacteria, M. tuberculosis drug resistance is acquired mainly through mutations in specific drug resistance-associated genes. The panel of mutations is highly diverse, but depends on the affected gene and M. tuberculosis genetic background. The variety of genetic profiles observed in drug-resistant clinical isolates underlines different evolutionary trajectories towards multiple drug resistance, although some mutation patterns are prominent. This review discusses the intrinsic processes that may influence drug resistance evolution in M. tuberculosis, such as mutation rate, drug resistance-associated mutations, fitness cost, compensatory mutations and epistasis. This knowledge should help to better predict the risk of emergence of highly resistant M. tuberculosis strains and to develop new tools and strategies to limit the development and spread of MDR and XDR strains.
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Affiliation(s)
- Quang Huy Nguyen
- Department of Pharmacological, Medical and Agronomical BiotechnologyUniversity of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
| | - Lucie Contamin
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Thi Van Anh Nguyen
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Anne‐Laure Bañuls
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
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138
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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139
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Hicks ND, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune SM. Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance. Nat Microbiol 2018; 3:1032-1042. [PMID: 30082724 PMCID: PMC6233875 DOI: 10.1038/s41564-018-0218-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/09/2023]
Abstract
The global epidemic of drug-resistant tuberculosis is a catastrophic example of how antimicrobial resistance is undermining the public health gains made possible by combination drug therapy. Recent evidence points to unappreciated bacterial factors that accelerate the emergence of drug resistance. In a genome-wide association study of Mycobacterium tuberculosis isolates from China, we find mutations in the gene encoding the transcription factor prpR enriched in drug-resistant strains. prpR mutations confer conditional drug tolerance to three of the most effective classes of antibiotics by altering propionyl-CoA metabolism. prpR-mediated drug tolerance is carbon-source dependent, and while readily detectable during infection of human macrophages, is not captured by standard susceptibility testing. These data define a previously unrecognized and clinically prevalent class of M. tuberculosis variants that undermine antibiotic efficacy and drive drug resistance.
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Affiliation(s)
- Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhili Chang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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140
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Hsieh MH, Ou CY, Hsieh WY, Kao HF, Lee SW, Wang JY, Wu LSH. Functional Analysis of Genetic Variations in Surfactant Protein D in Mycobacterial Infection and Their Association With Tuberculosis. Front Immunol 2018; 9:1543. [PMID: 30013576 PMCID: PMC6036787 DOI: 10.3389/fimmu.2018.01543] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 01/02/2023] Open
Abstract
Surfactant proteins (SPs)-A and -D are C-type lectins of the collectin family and function in the clearance of infectious particles in the lungs. Some polymorphisms of SPs that give rise to amino acid changes have been found to affect their function. Several SP-A gene polymorphisms have been reported to be associated with respiratory infection diseases, such as tuberculosis (TB). However, the relationship between surfactant proteins D (SP-D) polymorphisms and TB is still unclear. To study the associations between SP-D polymorphisms and TB, the correlations of SP-D polymorphisms with TB were examined in a case-control study, which included 364 patients with TB and 177 control subjects. In addition, we cloned two major SP-D exonic polymorphism C92T (rs721917) and A538G (rs2243639) constructs and used these for in vitro assays. The effects of SP-D polymorphisms on agglutination and other interactions with Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) were evaluated. In comparison with SP-D 92C (amino acid residue 16, Threonine), our results showed that SP-D 92T (amino acid residue 16, Methionine) had a lower binding ability to M. bovis BCG, a lower capacity to inhibit phagocytosis, lesser aggregation, poorer survival of bacillus Calmette-Guérin (BCG)-infected MH-S cells, and less inhibition of intracellular growth of M. bovis BCG. The case-control association study showed that the 92T homozygous genotype was a risk factor for TB. However, a lesser effect was seen for polymorphism A538G. In conclusion, the results of functional and genetic analyses of SP-D variants consistently showed that the SP-D 92T variant increased susceptibility to TB, which further confirmed the role of SP-D in pulmonary innate immunity against mycobacterial infection.
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Affiliation(s)
- Miao-Hsi Hsieh
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Ying Ou
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Yu Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Fang Kao
- Allergy and Clinical Immunology Research (ACIR) Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Wei Lee
- Chest Medicine, General Taoyuan Hospital, Taoyuan, Taiwan
| | - Jiu-Yao Wang
- Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Respiratory Research, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lawrence S H Wu
- Allergy and Clinical Immunology Research (ACIR) Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
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141
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Mortimer TD, Grad YH. Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Ann N Y Acad Sci 2018; 1435:93-109. [PMID: 29876934 DOI: 10.1111/nyas.13871] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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142
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Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar J, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 2018; 50:849-856. [PMID: 29785015 PMCID: PMC6143168 DOI: 10.1038/s41588-018-0117-9] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
Abstract
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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Affiliation(s)
- Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
| | - Paul McAdam
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Hoang Thanh Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Artika P Nath
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yik Ying Teo
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Michael Inouye
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Birat-Nepal Medical Trust, Kathmandu, Nepal
| | - Sarah J Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.
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143
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Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 2018. [PMID: 29785015 DOI: 10.1038/s41588-018-0117-9.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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144
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Zeng X, Kwok JSL, Yang KY, Leung KSS, Shi M, Yang Z, Yam WC, Tsui SKW. Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance. BMC Genomics 2018; 19:365. [PMID: 29769016 PMCID: PMC5956929 DOI: 10.1186/s12864-018-4734-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. Results Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance. A total of 20 region markers containing genes and intergenic regions (IGRs) with significant statistical correlation with antibiotic resistance were revealed, four of which have been previously reported to be associated with drug resistance. In addition, 83 point markers containing frameshift (FS) mutations and IGR indels were also identified independently based on differences in their incidence rates between drug-sensitive and -resistant strains. Among the 83 point markers, eight indels were detected in known drug-associated genes or IGRs. Furthermore, the overlap between 20 region markers and 83 point markers further indicated their associations with drug resistance. The markers identified were involved in essential bacterial metabolic functions, including cell wall and transmembrane transporter functions. A strong correlation between FS mutations and mutations in DNA repair genes including I21V in alkA, R48G in mutT4 and P2R in nth was also found. Conclusions This study identified a set of novel genetic markers with FS mutations and IGR indels associated with MTB drug resistance, which greatly broadens the pool of mutations related to MTB drug resistance. This insight may be important in identifying novel mechanisms of drug resistance in MTB. Electronic supplementary material The online version of this article (10.1186/s12864-018-4734-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhiyuan Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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145
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DNA Replication Fidelity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1019:247-262. [PMID: 29116639 DOI: 10.1007/978-3-319-64371-7_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis is genetically isolated, with no evidence for horizontal gene transfer or the acquisition of episomal genetic information in the modern evolution of strains of the Mycobacterium tuberculosis complex. When considered in the context of the specific features of the disease M. tuberculosis causes (e.g., transmission via cough aerosol, replication within professional phagocytes, subclinical persistence, and stimulation of a destructive immune pathology), this implies that to understand the mechanisms ensuring preservation of genomic integrity in infecting mycobacterial populations is to understand the source of genetic variation, including the emergence of microdiverse sub-populations that may be linked to the acquisition of drug resistance. In this chapter, we focus on mechanisms involved in maintaining DNA replication fidelity in M. tuberculosis, and consider the potential to target components of the DNA replication machinery as part of novel therapeutic regimens designed to curb the emerging threat of drug-resistance.
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146
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Carey AF, Rock JM, Krieger IV, Chase MR, Fernandez-Suarez M, Gagneux S, Sacchettini JC, Ioerger TR, Fortune SM. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog 2018; 14:e1006939. [PMID: 29505613 PMCID: PMC5854444 DOI: 10.1371/journal.ppat.1006939] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 01/25/2023] Open
Abstract
Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for most phenotypic differences among Mtb strains remains unknown. To investigate the basis of strain variation in Mtb, we performed genome-wide transposon mutagenesis coupled with next-generation sequencing (TnSeq) for a panel of Mtb clinical isolates and the reference strain H37Rv to compare genetic requirements for in vitro growth across these strains. We developed an analytic approach to identify quantitative differences in genetic requirements between these genetically diverse strains, which vary in genomic structure and gene content. Using this methodology, we found differences between strains in their requirements for genes involved in fundamental cellular processes, including redox homeostasis and central carbon metabolism. Among the genes with differential requirements were katG, which encodes the activator of the first-line antitubercular agent isoniazid, and glcB, which encodes malate synthase, the target of a novel small-molecule inhibitor. Differences among strains in their requirement for katG and glcB predicted differences in their response to these antimicrobial agents. Importantly, these strain-specific differences in antibiotic response could not be predicted by genetic variants identified through whole genome sequencing or by gene expression analysis. Our results provide novel insight into the basis of variation among Mtb strains and demonstrate that TnSeq is a scalable method to predict clinically important phenotypic differences among Mtb strains.
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Affiliation(s)
- Allison F. Carey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jeremy M. Rock
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Michael R. Chase
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marta Fernandez-Suarez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (SMF); (TRI)
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (SMF); (TRI)
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147
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Ng KC, Meehan CJ, Torrea G, Goeminne L, Diels M, Rigouts L, de Jong BC, André E. Potential Application of Digitally Linked Tuberculosis Diagnostics for Real-Time Surveillance of Drug-Resistant Tuberculosis Transmission: Validation and Analysis of Test Results. JMIR Med Inform 2018; 6:e12. [PMID: 29487047 PMCID: PMC5849801 DOI: 10.2196/medinform.9309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the highest-mortality infectious disease in the world and the main cause of death related to antimicrobial resistance, yet its surveillance is still paper-based. Rifampicin-resistant TB (RR-TB) is an urgent public health crisis. The World Health Organization has, since 2010, endorsed a series of rapid diagnostic tests (RDTs) that enable rapid detection of drug-resistant strains and produce large volumes of data. In parallel, most high-burden countries have adopted connectivity solutions that allow linking of diagnostics, real-time capture, and shared repository of these test results. However, these connected diagnostics and readily available test results are not used to their full capacity, as we have yet to capitalize on fully understanding the relationship between test results and specific rpoB mutations to elucidate its potential application to real-time surveillance. OBJECTIVE We aimed to validate and analyze RDT data in detail, and propose the potential use of connected diagnostics and associated test results for real-time evaluation of RR-TB transmission. METHODS We selected 107 RR-TB strains harboring 34 unique rpoB mutations, including 30 within the rifampicin resistance-determining region (RRDR), from the Belgian Coordinated Collections of Microorganisms, Antwerp, Belgium. We subjected these strains to Xpert MTB/RIF, GenoType MTBDRplus v2.0, and Genoscholar NTM + MDRTB II, the results of which were validated against the strains' available rpoB gene sequences. We determined the reproducibility of the results, analyzed and visualized the probe reactions, and proposed these for potential use in evaluating transmission. RESULTS The RDT probe reactions detected most RRDR mutations tested, although we found a few critical discrepancies between observed results and manufacturers' claims. Based on published frequencies of probe reactions and RRDR mutations, we found specific probe reactions with high potential use in transmission studies: Xpert MTB/RIF probes A, Bdelayed, C, and Edelayed; Genotype MTBDRplus v2.0 WT2, WT5, and WT6; and Genoscholar NTM + MDRTB II S1 and S3. Inspection of probe reactions of disputed mutations may potentially resolve discordance between genotypic and phenotypic test results. CONCLUSIONS We propose a novel approach for potential real-time detection of RR-TB transmission through fully using digitally linked TB diagnostics and shared repository of test results. To our knowledge, this is the first pragmatic and scalable work in response to the consensus of world-renowned TB experts in 2016 on the potential of diagnostic connectivity to accelerate efforts to eliminate TB. This is evidenced by the ability of our proposed approach to facilitate comparison of probe reactions between different RDTs used in the same setting. Integrating this proposed approach as a plug-in module to a connectivity platform will increase usefulness of connected TB diagnostics for RR-TB outbreak detection through real-time investigation of suspected RR-TB transmission cases based on epidemiologic linking.
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Affiliation(s)
- Kamela Charmaine Ng
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor Joseph Meehan
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Gabriela Torrea
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Léonie Goeminne
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke Catherine de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel André
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,Laboratory of Clinical Bacteriology and Mycology, Katholieke Universiteit Leuven, Leuven, Belgium
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148
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149
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Manson AL, Abeel T, Galagan JE, Sundaramurthi JC, Salazar A, Gehrmann T, Shanmugam SK, Palaniyandi K, Narayanan S, Swaminathan S, Earl AM. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics. Clin Infect Dis 2018; 64:1494-1501. [PMID: 28498943 PMCID: PMC5434337 DOI: 10.1093/cid/cix169] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background. India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3. Methods. We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance. Results. Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance. Conclusions. In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.
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Affiliation(s)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - James E Galagan
- Department of Biomedical Engineering, and.,National Emerging Infectious Diseases Laboratory, Boston University, Massachusetts
| | | | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | - Thies Gehrmann
- Delft Bioinformatics Lab, Delft University of Technology, The Netherlands
| | | | | | | | | | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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150
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Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018; 111:205-211. [PMID: 29432978 DOI: 10.1016/j.ygeno.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 11/16/2022]
Abstract
In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shannon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms. These methods are generic and can be implemented for analysis of any organism. We have shown usefulness of these approaches for analysis of Mycobacterium tuberculosis and Escherichia coli isolates. We were able to identify a minimal set of 18 SNPs that can be used as molecular markers for phylogroup based classification and 8 SNPs for pathogroup based classification of E. coli.
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Affiliation(s)
- Tanmoy Roychowdhury
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vinod Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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