9 results on '"Fyfe, Janet"'
Search Results
2. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history.
- Author
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Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L, Gehre F, Sanoussi CN, Antonio M, Affolabi D, Fyfe J, Beckert P, Niemann S, Alabi AS, Grobusch MP, Kobbe R, Parkhill J, Beisel C, Fenner L, Böttger EC, Meehan CJ, Harris SR, de Jong BC, Yeboah-Manu D, and Brites D
- Subjects
- Africa, Eastern, Africa, Western, Evolution, Molecular, Genome, Bacterial, High-Throughput Nucleotide Sequencing, Humans, Mycobacterium tuberculosis genetics, Mycobacterium tuberculosis isolation & purification, Phylogeny, Phylogeography, Drug Resistance, Bacterial, Mycobacterium tuberculosis classification, Tuberculosis microbiology, Whole Genome Sequencing methods
- Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto , as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum . Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum , and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
- Published
- 2021
- Full Text
- View/download PDF
3. Molecular epidemiology of tuberculosis in Tasmania and genomic characterisation of its first known multi-drug resistant case.
- Author
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Gautam SS, Mac Aogáin M, Cooley LA, Haug G, Fyfe JA, Globan M, and O'Toole RF
- Subjects
- Adolescent, Adult, Aged, Antitubercular Agents pharmacology, Antitubercular Agents therapeutic use, Child, Child, Preschool, Female, Humans, Infant, Male, Microbial Sensitivity Tests, Middle Aged, Mycobacterium tuberculosis drug effects, Phylogeny, Tasmania epidemiology, Tuberculosis drug therapy, Tuberculosis microbiology, Tuberculosis, Multidrug-Resistant drug therapy, Tuberculosis, Multidrug-Resistant microbiology, Young Adult, Genome, Bacterial, Molecular Epidemiology, Mycobacterium tuberculosis genetics, Tuberculosis epidemiology, Tuberculosis, Multidrug-Resistant epidemiology
- Abstract
Background: The origin and spread of tuberculosis (TB) in Tasmania and the types of strains of Mycobacterium tuberculosis complex (MTBC) present in the population are largely unknown., Objective: The aim of this study was to perform the first genomic analysis of MTBC isolates from Tasmania to better understand the epidemiology of TB in the state., Methods: Whole-genome sequencing was performed on cultured isolates of MTBC collected from 2014-2016. Single-locus variant analysis was applied to determine the phylogeny of the isolates and the presence of drug-resistance mutations. The genomic data were then cross-referenced against public health surveillance records on each of the cases., Results: We determined that 83.3% of TB cases in Tasmania from 2014-2016 occurred in non-Australian born individuals. Two possible TB clusters were identified based on single locus variant analysis, one from November-December 2014 (n = 2), with the second from May-August 2015 (n = 4). We report here the first known isolate of multi-drug resistant (MDR) M. tuberculosis in Tasmania from 2016 for which we established its drug resistance mutations and potential overseas origin. In addition, we characterised a case of M. bovis TB in a Tasmanian-born person who presented in 2014, approximately 40 years after the last confirmed case in the state's bovids., Conclusions: TB in Tasmania is predominantly of overseas origin with genotypically-unique drug-susceptible isolates of M. tuberculosis. However, the state also exhibits features of TB that are observed in other jurisdictions, namely, the clustering of cases, and drug resistance. Early detection of TB and contact tracing, particularly of overseas-born cases, coordinated with rapid laboratory drug-susceptibility testing and molecular typing, will be essential for Tasmania to reach the World Health Organisation's TB eradication goals for low-incidence settings.
- Published
- 2018
- Full Text
- View/download PDF
4. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages.
- Author
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Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, and Gagneux S
- Subjects
- Genotype, Global Health, Humans, Mycobacterium tuberculosis isolation & purification, Phylogeography, Tuberculosis genetics, DNA, Bacterial analysis, Genomics methods, Mycobacterium tuberculosis classification, Mycobacterium tuberculosis genetics, Polymorphism, Genetic genetics, Tuberculosis microbiology
- Abstract
Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration., Competing Interests: Statement The authors have no competing interests as defined by Springer Nature, or other interests that might be perceived to influence the results and/or discussion reported in this paper.
- Published
- 2016
- Full Text
- View/download PDF
5. Molecular characterization of isoniazid-resistant Mycobacterium tuberculosis isolates collected in Australia.
- Author
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Lavender C, Globan M, Sievers A, Billman-Jacobe H, and Fyfe J
- Subjects
- Algorithms, Alleles, Australia, Cluster Analysis, Codon, DNA, Bacterial, Genes, Bacterial, Geography, Humans, Mutation, Mycobacterium tuberculosis classification, Mycobacterium tuberculosis isolation & purification, Open Reading Frames, Phylogeny, Polymerase Chain Reaction, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Antitubercular Agents pharmacology, Drug Resistance, Bacterial drug effects, Isoniazid pharmacology, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis genetics, Tuberculosis microbiology
- Abstract
Elucidation of the molecular basis of isoniazid (INH) resistance in Mycobacterium tuberculosis has led to the development of different genotypic approaches for the rapid detection of INH resistance in clinical isolates. Mutations in katG, in particular the S315T substitution, are responsible for INH resistance in a large proportion of tuberculosis cases. However, the frequency of the katG S315T substitution varies with population samples. In this study, 52 epidemiologically unrelated clinical INH-resistant M. tuberculosis isolates collected in Australia were screened for mutations at katG codon 315 and the fabG1-inhA regulatory region. Importantly, 52 INH-sensitive isolates, selected to reflect the geographic and genotypic diversity of the isolates, were also included for comparison. The katG S315T substitution and fabG1-inhA -15 C-to-T mutation were identified in 34 and 13 of the 52 INH-resistant isolates, respectively, and none of the INH-sensitive isolates. Three novel katG mutations, D117A, M257I, and G491C, were identified in three INH-resistant strains with a wild-type katG codon 315, fabG1-inhA regulatory region, and inhA structural gene. When analyzed for possible associations between resistance mechanisms, resistance phenotype, and genotypic groups, it was found that neither the katG S315T nor fabG1-inhA -15 C-to-T mutation clustered with any one genotypic group, but that the -15 C-to-T substitution was associated with isolates with intermediate INH resistance and isolates coresistant to ethionamide. In total, 90.4% of unrelated INH-resistant isolates could be identified by analysis of just two loci: katG315 and the fabG1-inhA regulatory region.
- Published
- 2005
- Full Text
- View/download PDF
6. MYCOBACTERIUM PINNIPEDII TUBERCULOSIS IN A FREE-RANGING AUSTRALIAN FUR SEAL (ARCTOCEPHALUS PUSILLUS DORIFERUS) IN SOUTH AUSTRALIA
- Author
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Boardman, Wayne S. J., Shephard, Lisa, Bastian, Ivan, Globan, Maria, Fyfe, Janet A. M., Cousins, Debby V., Machado, Aaron, and Woolford, Lucy
- Published
- 2014
7. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set
- Author
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Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla del Valle, Miriam, Fyfe, Janet, García-García, Lourdes, Rastogi, Nalin, Sola, Christophe, Zozio, Thierry, Guerrero, Marta Inírida, León, Clara Inés, Crabtree, Jonathan, Angiuoli, Sam, Eisenach, Kathleen D., Durmaz, Riza, Joloba, Moses L., Rendón, Adrian, Sifuentes-Osornio, José, Ponce de León, Alfredo, Cave, M. Donald, Fleischmann, Robert, Whittam, Thomas S., and Alland, David
- Subjects
Errata ,Geography ,DNA fingerprinting ,DNA sequence ,Minisatellite Repeats ,Mycobacterium tuberculosis ,Microbiología ,Enfermedades ,Polymorphism, Single Nucleotide ,Bacterial Typing Techniques ,Evolución & genética ,Evolution, Molecular ,Species Specificity ,Genes, Bacterial ,Multigene Family ,Humans ,Tuberculosis ,Genetic variability ,Controlled study ,Bacteria (microorganisms) ,Algorithms ,Population Genetics and Evolution - Abstract
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis. Copyright © 2006, American Society for Microbiology. All Rights Reserved.
- Published
- 2005
8. Pulmonary extensively drug-resistant tuberculosis in Melbourne: local control of a global health challenge.
- Author
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Tramontana, Adrian R., Leslie, David E., Nolan, Aine, Globan, Maria, Fyfe, Janet M., Denholm, Justin T., and Guy, Stephen D.
- Abstract
The article presents a case study of a 21-year-old HIV-negative man diagnosed with pulmonary extensively drug-resistant tuberculosis (TB) discussing the use of drugs such as amikacin and moxifloxacin for treatment; the side effects during the treatment; and monitoring of patient for recurrence.
- Published
- 2018
- Full Text
- View/download PDF
9. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
- Author
-
Coscolla, Mireia, Gagneux, Sebastien, Menardo, Fabrizio, Loiseau, Chloé, Ruiz-Rodriguez, Paula, Borrell, Sonia, Otchere, Isaac Darko, Asante-Poku, Adwoa, Asare, Prince, Sánchez-Busó, Leonor, Gehre, Florian, Sanoussi, C N'Dira, Antonio, Martin, Affolabi, Dissou, Fyfe, Janet, Beckert, Patrick, Niemann, Stefan, Alabi, Abraham S, Grobusch, Martin P, Kobbe, Robin, Parkhill, Julian, Beisel, Christian, Fenner, Lukas, Böttger, Erik C, Meehan, Conor J, Harris, Simon R, De Jong, Bouke C, Yeboah-Manu, Dorothy, and Brites, Daniela
- Subjects
Mycobacterium africanum ,Whole Genome Sequencing ,mycobacteria ,High-Throughput Nucleotide Sequencing ,Mycobacterium tuberculosis ,Africa, Eastern ,3. Good health ,diversity ,Evolution, Molecular ,Africa, Western ,Phylogeography ,evolution ,Drug Resistance, Bacterial ,Humans ,Tuberculosis ,genome ,Genome, Bacterial ,Phylogeny - Abstract
Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as Mycobacterium africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
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