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Matthews MC, Cooke DM, Kerr TJ, Loxton AG, Warren RM, Ghielmetti G, Streicher EM, Witte CS, Miller MA, Goosen WJ. Evidence of Mycobacterium bovis DNA in shared water sources at livestock-wildlife-human interfaces in KwaZulu-Natal, South Africa. Front Vet Sci 2025; 12:1483162. [PMID: 40093619 PMCID: PMC11907651 DOI: 10.3389/fvets.2025.1483162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 02/05/2025] [Indexed: 03/19/2025] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) including Mycobacterium bovis (M. bovis), which primarily affects animal hosts; however, it is also capable of causing zoonotic infections in humans. Direct contact with infected animals or their products is the primary mode of transmission. However, recent research suggests that M. bovis can be shed into the environment, potentially playing an under-recognized role in the pathogen' spread. Further investigation into indirect transmission of M. bovis, employing a One Health approach, is necessary to evaluate its epidemiological significance. However, current methods are not optimized for identifying M. bovis in complex environmental samples. Nevertheless, in a recent study, a combination of molecular techniques, including next-generation sequencing (NGS), was able to detect M. bovis DNA in the environment to investigate epidemiological questions. The aim of this study was, therefore, to apply a combination of culture-independent methods, such as targeted NGS (tNGS), to detect pathogenic mycobacteria, including M. bovis, in water sources located in a rural area of KwaZulu-Natal (KZN), South Africa. This area was selected based on the high burden of MTBC in human and animal populations. Water samples from 63 sites were screened for MTBC DNA by extracting DNA and performing hsp65 PCR amplification, followed by Sanger amplicon sequencing (SAS). Sequences were compared to the National Centre for Biotechnology Information (NCBI) database for genus or species-level identification. Samples confirmed to contain mycobacterial DNA underwent multiple PCRs (hsp65, rpoB, and MAC hsp65) and sequencing with Oxford Nanopore Technologies (ONT) tNGS. The ONT tNGS consensus sequences were compared to a curated in-house database to identify mycobacteria to genus, species, or species complex (e.g., MTBC) level for each sample site. Additional screening for MTBC DNA was performed using the GeneXpert® MTB/RIF Ultra (GXU) qPCR assay. Based on GXU, hsp65 SAS, and ONT tNGS results, MTBC DNA was present in 12 of the 63 sites. The presence of M. bovis DNA was confirmed at 4 of the 12 sites using downstream polymerase chain reaction (PCR)-based methods. However, further studies are required to determine if environmental M. bovis is viable. These results support further investigation into the role that shared water sources may play in TB epidemiology.
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Affiliation(s)
- Megan C Matthews
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Deborah M Cooke
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J Kerr
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G Loxton
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Giovanni Ghielmetti
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse, Zürich, Switzerland
| | - Elizabeth M Streicher
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Carmel S Witte
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michele A Miller
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J Goosen
- South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
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Coetzee JL, Kriel NL, Loubser J, Dippenaar A, Sampson SL, Malherbe ST, Mouton JM. Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations. Sci Rep 2024; 14:27686. [PMID: 39532967 PMCID: PMC11557868 DOI: 10.1038/s41598-024-79389-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 11/08/2024] [Indexed: 11/16/2024] Open
Abstract
Current tuberculosis (TB) treatment is typically effective against drug-susceptible Mycobacterium tuberculosis, but can fail due to acquired drug resistance or phenotypic resistance. M. tuberculosis persisters, a subpopulation of viable but non-replicating (VBNR) antibiotic-tolerant bacteria, are thought to contribute to poor TB treatment outcomes. In this exploratory study, we investigated treatment-naïve drug-susceptible clinical isolates collected from people with TB, who subsequently had unsuccessful treatment outcomes. These were compared to isolates from cured individuals in terms of their ability to form VBNR subpopulations. Clinical isolates from individuals with unfavorable treatment outcomes form larger subpopulations of VBNR M. tuberculosis (2.67-13.71%) than clinical isolates from cured cases (0- 1.63%) following infection of THP-1 macrophages. All isolates were drug susceptible based on phenotypic and genotypic analysis. Whole genome sequencing identified 23 non-synonymous genomic variants shared by treatment failure clinical isolates, that were not present in isolates from cured cases. This exploratory study highlights the ability of treatment-naïve clinical isolates to form heterogeneous populations containing VBNR M. tuberculosis. We also demonstrate that clinical isolates from individuals with unsuccessful treatment outcomes form higher percentages of VBNR M. tuberculosis. The findings of this exploratory study suggest that an increased propensity to form VBNR subpopulations may impact TB treatment outcome.
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Affiliation(s)
- Julian L Coetzee
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Nastassja L Kriel
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa.
| | - Johannes Loubser
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Anzaan Dippenaar
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Samantha L Sampson
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Stephanus T Malherbe
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
| | - Jacoba M Mouton
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, Cape Town, 7505, South Africa
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3
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Klopper M, van der Merwe CJ, van der Heijden YF, Folkerts M, Loubser J, Streicher EM, Mekler K, Hayes C, Engelthaler DM, Metcalfe JZ, Warren RM. The Hidden Epidemic of Isoniazid-Resistant Tuberculosis in South Africa. Ann Am Thorac Soc 2024; 21:1391-1397. [PMID: 38935769 PMCID: PMC11451881 DOI: 10.1513/annalsats.202312-1076oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 06/29/2024] Open
Abstract
Rationale: Isoniazid-resistant tuberculosis (Hr-TB) is often overlooked in diagnostic algorithms because of reliance on first-line molecular assays testing only for rifampicin resistance. Objectives: To determine the prevalence, outcomes, and molecular mechanisms associated with rifampin-susceptible, isoniazid-resistant TB (Hr-TB) in the Eastern Cape, South Africa. Methods: Between April 2016 and October 2017, sputum samples were collected from patients with rifampin-susceptible TB at baseline and at Weeks 7 and 23 of drug-susceptible TB treatment. We performed isoniazid phenotypic and genotypic drug susceptibility testing, including FluoroTypeMTBDR, Sanger sequencing, targeted next-generation sequencing, and whole-genome sequencing. Results: We analyzed baseline isolates from 766 patients with rifampin-susceptible TB. Of 89 patients (11.7%) who were found to have Hr-TB, 39 (44%) had canonical katG or inhA promoter mutations; 35 (39%) had noncanonical katG mutations (including 5 with underlying large deletions); 4 (5%) had mutations in other candidate genes associated with isoniazid resistance. For 11 (12.4%), no cause of resistance was found. Conclusions: Among patients with rifampin-susceptible TB who were diagnosed using first-line molecular TB assays, there is a high prevalence of Hr-TB. Phenotypic drug susceptibility testing remains the gold standard. To improve the performance of genetic-based phenotyping tests, all isoniazid resistance-associated regions should be included, and such tests should have the ability to identify underlying mutations.
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Affiliation(s)
- Marisa Klopper
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | - Charnay J. van der Merwe
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town and University of Cape Town Lung Institute, Cape Town, South Africa
| | - Yuri F. van der Heijden
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
- The Aurum Institute, Johannesburg, South Africa
| | - Megan Folkerts
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | - Elizabeth M. Streicher
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
| | | | - Cindy Hayes
- National Health Laboratory Services, Port Elizabeth, South Africa; and
| | - David M. Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona
| | - John Z. Metcalfe
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, California
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, South Africa
- South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa
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Silva-Pereira TT, Soler-Camargo NC, Guimarães AMS. Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures. Microbiol Spectr 2024; 12:e0228923. [PMID: 38230932 PMCID: PMC10871547 DOI: 10.1128/spectrum.02289-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
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Affiliation(s)
- Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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5
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Roos EO, Loubser J, Kerr TJ, Dippenaar A, Streicher E, Olea-Popelka F, Robbe-Austerman S, Stuber T, Buss P, de Klerk-Lorist LM, Warren RM, van Helden PD, Parsons SD, Miller MA. Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa. One Health 2023; 17:100654. [PMID: 38283183 PMCID: PMC10810834 DOI: 10.1016/j.onehlt.2023.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/08/2023] [Indexed: 01/30/2024] Open
Abstract
Background Mycobacterium bovis forms part of the Mycobacterium tuberculosis complex and has an extensive host range and zoonotic potential. Various genotyping methods (e.g., spoligotyping) have been used to describe the molecular epidemiology of M. bovis. Advances in whole genome sequencing (WGS) have increased resolution to enable detection of genomic variants to the level of single nucleotide polymorphisms. This is especially relevant to One Health research on tuberculosis which benefits by being able to use WGS to identify epidemiologically linked cases, especially recent transmission. The use of WGS in molecular epidemiology has been extensively used in humans and cattle but is limited in wildlife. This approach appears to overcome the limitations of conventional genotyping methods due to lack of genetic diversity in M. bovis. Methods This pilot study investigated the spoligotype and WGS of M. bovis isolates (n = 7) from wildlife in Marloth Park (MP) and compared these with WGS data from other South African M. bovis isolates. In addition, the greater resolution of WGS was used to explore the phylogenetic relatedness of M. bovis isolates in neighbouring wildlife populations. Results The phylogenetic analyses showed the closest relatives to the seven isolates from MP were isolates from wildlife in Kruger National Park (KNP), which shares a border with MP. However, WGS data indicated that the KNP and MP isolates formed two distinct clades, even though they had similar spoligotypes and identical in silico genetic regions of difference profiles. Conclusions Mycobacterium bovis isolates from MP were hypothesized to be directly linked to KNP wildlife, based on spoligotyping. However, WGS indicated more complex epidemiology. The presence of two distinct clades which were genetically distinct (SNP distance of 19-47) and suggested multiple transmission events. Therefore, WGS provided new insight into the molecular epidemiology of the M. bovis isolates from MP and their relationship to isolates from KNP. This approach will facilitate greater understanding of M. bovis transmission at wildlife-livestock-human interfaces and advances One Health research on tuberculosis, especially across different host species.
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Affiliation(s)
- Eduard O. Roos
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Johannes Loubser
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Tanya J. Kerr
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Elizma Streicher
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Francisco Olea-Popelka
- Department of Pathology and Laboratory Medicine, Schulich Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Private Bag X402, Skukuza, 1350, South Africa
| | - Lin-Mari de Klerk-Lorist
- Department of Agriculture Land Reform and Rural Development, Office of the State Veterinarian, Kruger National Park, PO Box 12, Skukuza, 1350, South Africa
| | - Robin M. Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Paul D. van Helden
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Sven D.C. Parsons
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Michele A. Miller
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
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6
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Zhang X, Lam C, Martinez E, Sim E, Crighton T, Marais BJ, Sintchenko V. Genomic markers of drug resistance in Mycobacterium tuberculosis populations with minority variants. J Clin Microbiol 2023; 61:e0048523. [PMID: 37750734 PMCID: PMC10595065 DOI: 10.1128/jcm.00485-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
Minority variants of Mycobacterium tuberculosis harboring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug-resistant within-host subpopulations and the frequency of resistance-conferring mutations in minority variants remains limited. M. tuberculosis sequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance-conferring minority variants were identified using LoFreq, and mixed populations of different M. tuberculosis strains (≥100 SNPs apart) were examined using QuantTB. A total of 1831 routinely sequenced M. tuberculosis strains were included in the analysis. Drug resistance-conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high-confidence drug resistance-conferring mutations were 1.5 times more common when the majority strains were drug resistant. Mixed M. tuberculosis strain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high-confidence drug resistance-conferring mutations were more frequently detected in mixed M. tuberculosis strain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; P = 0.01). Drug-resistant minority variants require monitoring in settings that implement routine M. tuberculosis sequencing. The frequency with which drug-resistant minority variants are detected is likely influenced by pre-culture requirement. Culture-independent sequencing methods should provide a more accurate reflection of drug-resistant subpopulations.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
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7
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Otum CC, Rivière E, Barnard M, Loubser J, Williams MJ, Streicher EM, Van Rie A, Warren RM, Klopper M. Site-directed mutagenesis of Mycobacterium tuberculosis and functional validation to investigate potential bedaquiline resistance-causing mutations. Sci Rep 2023; 13:9212. [PMID: 37280265 DOI: 10.1038/s41598-023-35563-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/20/2023] [Indexed: 06/08/2023] Open
Abstract
Molecular detection of bedaquiline resistant tuberculosis is challenging as only a small proportion of mutations in candidate bedaquiline resistance genes have been statistically associated with phenotypic resistance. We introduced two mutations, atpE Ile66Val and Rv0678 Thr33Ala, in the Mycobacterium tuberculosis H37Rv reference strain using homologous recombineering or recombination to investigate the phenotypic effect of these mutations. The genotype of the resulting strains was confirmed by Sanger- and whole genome sequencing, and bedaquiline susceptibility was assessed by minimal inhibitory concentration (MIC) assays. The impact of the mutations on protein stability and interactions was predicted using mutation Cutoff Scanning Matrix (mCSM) tools. The atpE Ile66Val mutation did not elevate the MIC above the critical concentration (MIC 0.25-0.5 µg/ml), while the MIC of the Rv0678 Thr33Ala mutant strains (> 1.0 µg/ml) classifies the strain as resistant, confirming clinical findings. In silico analyses confirmed that the atpE Ile66Val mutation minimally disrupts the bedaquiline-ATP synthase interaction, while the Rv0678 Thr33Ala mutation substantially affects the DNA binding affinity of the MmpR transcriptional repressor. Based on a combination of wet-lab and computational methods, our results suggest that the Rv0678 Thr33Ala mutation confers resistance to BDQ, while the atpE Ile66Val mutation does not, but definite proof can only be provided by complementation studies given the presence of secondary mutations.
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Affiliation(s)
- Christian C Otum
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Emmanuel Rivière
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Monique Barnard
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Johannes Loubser
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Monique J Williams
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Elizabeth M Streicher
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin M Warren
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marisa Klopper
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
- Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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8
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Perumal R, Khan A, Naidoo K, Ngema SL, Nandlal L, Padayatchi N, Dookie N. Mycobacterium tuberculosis Intra-Host Evolution Among Drug-Resistant Tuberculosis Patients Failing Treatment. Infect Drug Resist 2023; 16:2849-2859. [PMID: 37193296 PMCID: PMC10182815 DOI: 10.2147/idr.s408976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Background Understanding Mycobacterium tuberculosis (Mtb) intra-host evolution of drug resistance is important for successful drug-resistant tuberculosis (DR-TB) treatment and control strategies. This study aimed to characterise the acquisition of genetic mutations and low-frequency variants associated with treatment-emergent Mtb drug resistance in longitudinally profiled clinical isolates from patients who experienced DR-TB treatment failure. Patients and Methods We performed deep Whole Genome Sequencing on 23 clinical isolates obtained longitudinally across nine timepoints from five patients who experienced DR-TB treatment failure enrolled in the CAPRISA 020 InDEX study. The minimum inhibitory concentrations (MICs) were established on the BACTEC™ MGIT 960™ instrument on 15/23 longitudinal clinical isolates for eight anti-TB drugs (rifampicin, isoniazid, ethambutol, levofloxacin, moxifloxacin, linezolid, clofazimine, bedaquiline). Results In total, 22 resistance associated mutations/variants were detected. We observed four treatment-emergent mutations in two out of the five patients. Emerging resistance to the fluoroquinolones was associated with 16- and 64-fold elevated levofloxacin (2-8 mg/L) and moxifloxacin (1-2 mg/L) MICs, respectively, resulting from the D94G/N and A90V variants in the gyrA gene. We identified two novel mutations associated with elevated bedaquiline MICs (>66-fold): an emerging frameshift variant (D165) on the Rv0678 gene and R409Q variant on the Rv1979c gene present from baseline. Conclusion Genotypic and phenotypic resistance to the fluoroquinolones and bedaquiline was acquired in two out of five patients who experienced DR-TB treatment failure. Deep sequencing of multiple longitudinal clinical isolates for resistance-associated mutations coupled with phenotypic MIC testing confirmed intra-host Mtb evolution.
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Affiliation(s)
- Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Senamile L Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
| | - Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, KwaZulu Natal, South Africa
- South African Medical Research Council (SAMRC) – CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, KwaZulu Natal, South Africa
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9
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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10
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Guo Q, Bi J, Lin Q, Ye T, Wang Z, Wang Z, Liu L, Zhang G. Whole Genome Sequencing Identifies Novel Mutations Associated With Bedaquiline Resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:807095. [PMID: 35694543 PMCID: PMC9184757 DOI: 10.3389/fcimb.2022.807095] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
Bedaquiline (BDQ), a new antitubercular agent, has been used to treat drug-resistant tuberculosis (TB). Although mutations in atpE, rv0678, and pepQ confer major resistance to BDQ, the mechanisms of resistance to BDQ in vitro and in clinical settings have not been fully elucidated. We selected BDQ-resistant mutants from 7H10 agar plates containing 0.5 mg/L BDQ (the critical concentration) and identified mutations associated with BDQ resistance through whole genome sequencing and Sanger sequencing. A total of 1,025 mutants were resistant to BDQ. We randomly selected 168 mutants for further analysis and discovered that 157/168 BDQ-resistant mutants harbored mutations in rv0678, which encodes a transcriptional regulator that represses the expression of the efflux pump, MmpS5–MmpL5. Moreover, we found two mutations with high frequency in rv0678 at nucleotide positions 286–287 (CG286–287 insertion; accounting for 26.8% [45/168]) and 198–199 (G198, G199 insertion, and G198 deletion; accounting for 14.3% [24/168]). The other mutations were dispersed covering the entire rv0678 gene. Moreover, we found that one new gene, glpK, harbors a G572 insertion; this mutation has a high prevalence (85.7%; 144/168) in the isolated mutants, and the minimum inhibitory concentration (MIC) assay demonstrated that it is closely associated with BDQ resistance. In summary, we characterized 168/1,025 mutants resistant to BDQ and found that mutations in rv0678 confer the primary mechanism of BDQ resistance. Moreover, we identified a new gene (glpK) involved in BDQ resistance. Our study offers new insights and valuable information that will contribute to rapid identification of BDQ-resistant isolates in clinical settings.
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Affiliation(s)
- Qinglong Guo
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Qiao Lin
- Department of Traditional Chinese Medicine, The Baoan People’s Hospital of Shenzhen, Shenzhen University, Shenzhen, China
| | - Taosheng Ye
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhongyuan Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Guoliang Zhang,
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11
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https://doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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12
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https:/doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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13
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022; 13:263. [PMID: 35205308 PMCID: PMC8872330 DOI: 10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Affiliation(s)
- Shiv kumar Rashmi Mudliar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Umay Kulsum
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Syed Beenish Rufai
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada;
- McGill International TB Center, Montreal, QC H4A 3J1, Canada
| | - Mika Umpo
- Tomo Riba Institute of Health & Medical Sciences, Naharlagun 791110, Arunachal Pradesh, India;
| | - Moi Nyori
- State TB Cell, Naharlagun 791110, Arunachal Pradesh, India;
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
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14
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Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis. J Clin Microbiol 2021; 60:e0190721. [PMID: 34757831 PMCID: PMC8769725 DOI: 10.1128/jcm.01907-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Pyrazinamide is an important component of both drug-susceptible and drug-resistant tuberculosis treatment regimens. Although approximately 50% of rifampin-resistant isolates are also resistant to pyrazinamide, pyrazinamide susceptibility testing is not routinely performed due to the challenging nature of the assay. We investigated the diagnostic accuracy of genotypic and phenotypic methods and explored the occurrence of pyrazinamide heteroresistance. We assessed pyrazinamide susceptibility among 358 individuals enrolled in the South African EXIT-RIF cohort using Sanger and targeted deep sequencing (TDS) of the pncA gene, whole-genome sequencing (WGS), and phenotypic drug susceptibility testing. We calculated the diagnostic accuracy of the different methods and investigated the prevalence and clinical impact of pncA heteroresistance. True pyrazinamide susceptibility status was assigned to each isolate using the Köser classification and expert rules. We observed 100% agreement across genotypic methods for detection of pncA fixed mutations; only TDS confidently identified three isolates (0.8%) with minor variants. For the 355 (99.2%) isolates that could be assigned true pyrazinamide status with confidence, phenotypic DST had a sensitivity of 96.5% (95% confidence interval [CI], 93.8 to 99.3%) and specificity of 100% (95% CI, 100 to 100%), both Sanger sequencing and WGS had a sensitivity of 97.1% (95% CI, 94.6 to 99.6%) and specificity of 97.8% (95% CI, 95.7 to 99.9%), and TDS had sensitivity of 98.8% (95% CI, 97.2 to 100%) and specificity of 97.8% (95% CI, 95.7 to 99.9%). We demonstrate high sensitivity and specificity for pyrazinamide susceptibility testing among all assessed genotypic methods. The prevalence of pyrazinamide heteroresistance in Mycobacterium tuberculosis isolates was lower than that identified for other first-line drugs.
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15
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Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2021; 131:102137. [PMID: 34673379 DOI: 10.1016/j.tube.2021.102137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022]
Abstract
Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.
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16
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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Yoshida S, Iwamoto T, Arikawa K, Sekizuka T, Kuroda M, Inoue Y, Mitarai S, Tsuji T, Tsuyuguchi K, Suzuki K. Bacterial population kinetics in heteroresistant Mycobacterium tuberculosis harbouring rare resistance-conferring mutations in gyrA and rpoB imply an epistatic interaction of mutations in a pre-XDR-TB patient. J Antimicrob Chemother 2021; 75:1722-1725. [PMID: 32303065 DOI: 10.1093/jac/dkaa109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Bacterial population kinetics of strains harbouring drug resistance-conferring mutations within a patient often show cryptic resistance in clinical practice. We report a case that showed emergence and dominance of Mycobacterium tuberculosis with uncommon rpoB and gyrA mutations, followed by an rpoC compensatory mutation, during treatment. METHODS A pre-XDR-TB patient showed heteroresistance to rifampicin and levofloxacin during treatment as a result of intermittent self-cessation. WGS was applied to investigate intra-host strain composition using five pairs of isolates from sputum samples. RESULTS The subclone in this study possessed rare mutations conferring resistance to rifampicin (rpoB V170F) and levofloxacin (gyrA S91P) and it rapidly outcompeted other subclones during treatment that included levofloxacin but not rifampicin (<7 days). The high-probability compensatory mutation rpoC V483A also emerged and became dominant subsequent to the rpoB V170F mutation. CONCLUSIONS To the best of our knowledge, this is the first case showing the emergence of such a rare variant that dominated the population within a patient during treatment of TB.
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Affiliation(s)
- Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Taisuke Tsuji
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Katsuhiro Suzuki
- Department of Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
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Genestet C, Hodille E, Barbry A, Berland JL, Hoffmann J, Westeel E, Bastian F, Guichardant M, Venner S, Lina G, Ginevra C, Ader F, Goutelle S, Dumitrescu O. Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathog 2021; 17:e1009643. [PMID: 34166469 PMCID: PMC8224949 DOI: 10.1371/journal.ppat.1009643] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genetic micro-diversity in clinical isolates may underline mycobacterial adaptation to tuberculosis (TB) infection and provide insights to anti-TB treatment response and emergence of resistance. Herein we followed within-host evolution of Mtb clinical isolates in two cohorts of TB patients, either with delayed Mtb culture conversion (> 2 months), or with fast culture conversion (< 2 months). We captured the genetic diversity of Mtb isolates obtained in each patient, by focusing on minor variants detected as unfixed single nucleotide polymorphisms (SNPs). To unmask antibiotic tolerant sub-populations, we exposed these isolates to rifampicin (RIF) prior to whole genome sequencing (WGS) analysis. Thanks to WGS, we detected at least 1 unfixed SNP within the Mtb isolates for 9/15 patients with delayed culture conversion, and non-synonymous (ns) SNPs for 8/15 patients. Furthermore, RIF exposure revealed 9 additional unfixed nsSNP from 6/15 isolates unlinked to drug resistance. By contrast, in the fast culture conversion cohort, RIF exposure only revealed 2 unfixed nsSNP from 2/20 patients. To better understand the dynamics of Mtb micro-diversity, we investigated the variant composition of a persistent Mtb clinical isolate before and after controlled stress experiments mimicking the course of TB disease. A minor variant, featuring a particular mycocerosates profile, became enriched during both RIF exposure and macrophage infection. The variant was associated with drug tolerance and intracellular persistence, consistent with the pharmacological modeling predicting increased risk of treatment failure. A thorough study of such variants not necessarily linked to canonical drug-resistance, but which are prone to promote anti-TB drug tolerance, may be crucial to prevent the subsequent emergence of resistance. Taken together, the present findings support the further exploration of Mtb micro-diversity as a promising tool to detect patients at risk of poorly responding to anti-TB treatment, ultimately allowing improved and personalized TB management. Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), bacteria that are able to persist inside the patient for many months or years, thus requiring long antibiotic treatments. Here we focused on TB patients with delayed response to treatment and we performed genetic characterization of Mtb isolates to search for sub-populations that may tolerate anti-TB drugs. We found that Mtb cultured from 9/15 patients contained different sub-populations, and in vitro drug exposure revealed Mtb sub-populations in 6/15 isolates, none related to known drug-resistance mechanisms. By contrast, drug exposure revealed Mtb sup-populations in 2/20 isolates in the control cohort of patients with fast culture conversion. Furthermore, we characterized a Mtb variant isolated from a sub-population growing in the presence of rifampicin (RIF), a major anti-TB drug. We found that this variant featured a modified lipidic envelope, and that it was able to develop in the presence of RIF and inside human macrophage cells. We performed pharmacological modelling and found that this kind of variant may be related to a poor response to treatment. In conclusion, searching for particular Mtb sub-populations may help to detect patients at risk of treatment failure and provide additional guidance for TB management.
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Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- * E-mail:
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Alexia Barbry
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Jean-Luc Berland
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Jonathan Hoffmann
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Emilie Westeel
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Fabiola Bastian
- Plateforme DTAMB, CNRS, Université Lyon 1, Villeurbanne, France
| | - Michel Guichardant
- CarMeN laboratory, INSA Lyon, INSERM U1060, INRA U1397, Université Lyon 1, Villeurbanne, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Christophe Ginevra
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Florence Ader
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Lyon, France
| | - Sylvain Goutelle
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Service pharmaceutique, Lyon, France
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
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19
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Melting the eis: Nondetection of Kanamycin Resistance Markers by Routine Diagnostic Tests and Identification of New eis Promoter Variants. Antimicrob Agents Chemother 2021; 65:e0250220. [PMID: 33903113 DOI: 10.1128/aac.02502-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eis promoter mutations can confer reduced Mycobacterium tuberculosis kanamycin susceptibility. GenoType MTBDRsl, a widely used assay evaluating this region, wrongly classified 17/410 isolates as eis promoter wild type. Six out of seventeen isolates harbored mutations known to confer kanamycin resistance, and the remainder harbored either novel eis promoter mutations (7/11) or disputed mutations (4/11). GenoType MTBDRsl can miss established and new variants that cause reduced susceptibility. These data highlight the importance of reflex phenotypic kanamycin testing.
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20
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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21
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Meiring C, Higgitt R, Dippenaar A, Roos E, Buss P, Hewlett J, Cooper D, Rogers P, Klerk‐Lorist L, Schalkwyk L, Hausler G, Helden P, Möller M, Warren R, Miller M. Characterizing epidemiological and genotypic features of
Mycobacterium bovis
infection in wild dogs (
Lycaon pictus
). Transbound Emerg Dis 2020. [DOI: 10.1111/tbed.13947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christina Meiring
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Roxanne Higgitt
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Anzaan Dippenaar
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Eduard Roos
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Peter Buss
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
| | - Jennie Hewlett
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
- Paraclinical Department Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
| | - Dave Cooper
- Ezemvelo KZN Wildlife Mtubatuba South Africa
| | - Peter Rogers
- Provet Wildlife Services & Companion Animal Hospital Hoedspruit South Africa
| | - Lin‐Mari Klerk‐Lorist
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Louis Schalkwyk
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Guy Hausler
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Paul Helden
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Marlo Möller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Rob Warren
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Michele Miller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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22
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Hjort K, Jurén P, Toro JC, Hoffner S, Andersson DI, Sandegren L. Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment. J Infect Dis 2020; 225:1011-1020. [PMID: 33045067 PMCID: PMC8921999 DOI: 10.1093/infdis/jiaa625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/08/2020] [Indexed: 11/15/2022] Open
Abstract
Abstract
Mycobacterium tuberculosis is one of the hardest to treat bacterial pathogens with a high capacity to develop antibiotic resistance by mutations. Here we have performed whole-genome sequencing of consecutive M. tuberculosis isolates obtained during 9 years from a patient with pulmonary tuberculosis. The infecting strain was isoniazid resistant and during treatment it stepwise accumulated resistance mutations to 8 additional antibiotics. Heteroresistance was common and subpopulations with up to 3 different resistance mutations to the same drug coexisted. Sweeps of different resistant clones dominated the population at different time points, always coupled to resistance mutations coinciding with changes in the treatment regimens. Resistance mutations were predominant and no hitch-hiking, compensatory, or virulence-increasing mutations were detected, showing that the dominant selection pressure was antibiotic treatment. The results highlight the dynamic nature of M. tuberculosis infection, population structure, and resistance evolution and the importance of rapid antibiotic susceptibility tests to battle this pathogen.
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Affiliation(s)
- Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Sven Hoffner
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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23
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Klopper M, Heupink TH, Hill-Cawthorne G, Streicher EM, Dippenaar A, de Vos M, Abdallah AM, Limberis J, Merker M, Burns S, Niemann S, Dheda K, Posey J, Pain A, Warren RM. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Med 2020; 18:24. [PMID: 32014024 PMCID: PMC6998097 DOI: 10.1186/s12916-019-1487-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. METHODS We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. RESULTS Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. CONCLUSION The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.
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Affiliation(s)
- Marisa Klopper
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Tim Hermanus Heupink
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Antwerp, Belgium
| | - Grant Hill-Cawthorne
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Elizabeth Maria Streicher
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Margaretha de Vos
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abdallah Musa Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Jason Limberis
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Scott Burns
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.,Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Robin Mark Warren
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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24
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Safi H, Gopal P, Lingaraju S, Ma S, Levine C, Dartois V, Yee M, Li L, Blanc L, Ho Liang HP, Husain S, Hoque M, Soteropoulos P, Rustad T, Sherman DR, Dick T, Alland D. Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance. Proc Natl Acad Sci U S A 2019; 116:19665-19674. [PMID: 31488707 PMCID: PMC6765255 DOI: 10.1073/pnas.1907631116] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a mechanism of genetically encoded but rapidly reversible drug tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of 7 cytosines (7C) in the glpK gene. Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multidrug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis-infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug tolerance, treatment failure, and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates.
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Affiliation(s)
- Hassan Safi
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103;
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Republic of Singapore
| | - Subramanya Lingaraju
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Shuyi Ma
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - Carly Levine
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Veronique Dartois
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Michelle Yee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Republic of Singapore
| | - Liping Li
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Landry Blanc
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Hsin-Pin Ho Liang
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - Seema Husain
- Genomics Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | - Mainul Hoque
- Genomics Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103
| | | | - Tige Rustad
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - David R Sherman
- Center for Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110
| | - David Alland
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ 07103;
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ 07103
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25
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Mouton JM, Heunis T, Dippenaar A, Gallant JL, Kleynhans L, Sampson SL. Comprehensive Characterization of the Attenuated Double Auxotroph Mycobacterium tuberculosisΔ leuDΔ panCD as an Alternative to H37Rv. Front Microbiol 2019; 10:1922. [PMID: 31481950 PMCID: PMC6710366 DOI: 10.3389/fmicb.2019.01922] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/05/2019] [Indexed: 01/04/2023] Open
Abstract
Although currently available model organisms such as Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) have significantly contributed to our understanding of tuberculosis (TB) biology, these models have limitations such as differences in genome size, growth rates and virulence. However, attenuated Mycobacterium tuberculosis strains may provide more representative, safer models to study M. tuberculosis biology. For example, the M. tuberculosis ΔleuDΔpanCD double auxotroph, has undergone rigorous in vitro and in vivo safety testing. Like other auxotrophic strains, this has subsequently been approved for use in biosafety level (BSL) 2 facilities. Auxotrophic strains have been assessed as models for drug-resistant M. tuberculosis and for studying latent TB. These offer the potential as safe and useful models, but it is important to understand how well these recapitulate salient features of non-attenuated M. tuberculosis. We therefore performed a comprehensive comparison of M. tuberculosis H37Rv and M. tuberculosisΔleuDΔpanCD. These strains demonstrated similar in vitro and intra-macrophage replication rates, similar responses to anti-TB agents and whole genome sequence conservation. Shotgun proteomics analysis suggested that M. tuberculosisΔleuDΔpanCD has a heightened stress response that leads to reduced bacterial replication during exposure to acid stress, which has been verified using a dual-fluorescent replication reporter assay. Importantly, infection of human peripheral blood mononuclear cells with the 2 strains elicited comparable cytokine production, demonstrating the suitability of M. tuberculosisΔleuDΔpanCD for immunological assays. We provide comprehensive evidence to support the judicious use of M. tuberculosisΔleuDΔpanCD as a safe and suitable model organism for M. tuberculosis research, without the need for a BSL3 facility.
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Affiliation(s)
- Jomien M Mouton
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tiaan Heunis
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anzaan Dippenaar
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - James L Gallant
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Section of Molecular Microbiology, Amsterdam Institute of Molecules, Medicines, and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Léanie Kleynhans
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha L Sampson
- Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Dippenaar A, De Vos M, Marx FM, Adroub SA, van Helden PD, Pain A, Sampson SL, Warren RM. Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting. INFECTION GENETICS AND EVOLUTION 2019; 75:103948. [PMID: 31276801 DOI: 10.1016/j.meegid.2019.103948] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/22/2019] [Accepted: 06/30/2019] [Indexed: 12/21/2022]
Abstract
Recurrent tuberculosis (TB) after successful TB treatment occurs due to endogenous reactivation (relapse) or exogenous reinfection. We revisited the conclusions of relapse in a high TB incidence setting that were drawn on the basis of IS6110 restriction fragment length polymorphism (RFLP) analysis in a large retrospective cohort study in suburban Cape Town, South Africa. Using whole genome sequencing (WGS), we undertook pair-wise genome comparison of Mycobacterium tuberculosis strains cultured from diagnostic sputum samples collected at the index and recurrent TB episode for 25 recurrent TB cases who had been classified as relapse based on identical DNA fingerprint patterns in the earlier study. We found that paired strain genome sequences were identical or showed minimal variant differences in 22 of 25 recurrent TB cases, consistent with relapse. One showed 20 variant differences, suggestive of exogenous reinfection. Two of the 25 had mixed infections, each with the index episode strain detected as the dominant strain at recurrence in one of these patients, the minority strain harboured drug-resistance conferring mutations (rpoB, katG). In conclusion, our study highlights the additional value of WGS for investigating recurrent TB in settings with high infection pressure and closely related circulating strains, where the extent of re- and mixed infection may be underestimated.
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Affiliation(s)
- Anzaan Dippenaar
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Margaretha De Vos
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florian M Marx
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; DST-NRF South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Sabir A Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Paul D van Helden
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samantha L Sampson
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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27
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Nimmo C, Shaw LP, Doyle R, Williams R, Brien K, Burgess C, Breuer J, Balloux F, Pym AS. Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC Genomics 2019; 20:389. [PMID: 31109296 PMCID: PMC6528373 DOI: 10.1186/s12864-019-5782-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Background Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. Results DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. Conclusions Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating. Electronic supplementary material The online version of this article (10.1186/s12864-019-5782-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK. .,Africa Health Research Institute, Durban, South Africa.
| | - Liam P Shaw
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Nuffield Department of Clinical Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Ronan Doyle
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | - Carrie Burgess
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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28
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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: 0.3] [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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29
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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: 38] [Impact Index Per Article: 6.3] [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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30
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Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, van Crevel R, Alisjahbana B. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. J Glob Antimicrob Resist 2019; 16:170-177. [DOI: 10.1016/j.jgar.2018.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/06/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022] Open
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31
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Clofazimine Exposure In Vitro Selects Efflux Pump Mutants and Bedaquiline Resistance. Antimicrob Agents Chemother 2019; 63:AAC.02141-18. [PMID: 30642938 DOI: 10.1128/aac.02141-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 12/31/2018] [Indexed: 11/20/2022] Open
Abstract
Six in vitro clofazimine-resistant spontaneous mutants obtained from a wild-type or pyrazinamide-resistant ATCC reference strain were selected to evaluate bedaquiline cross-resistance. The reverse was conducted for bedaquiline mutants. All clofazimine mutants harboring an rv0678 mutation displayed phenotypic cross-resistance. We observed the same for rv0678 bedaquiline mutants; however, atpE bedaquiline mutants showed no phenotypic cross-resistance. This confirms that upfront clofazimine usage may impact subsequent bedaquiline use due to a shared efflux resistance pathway.
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32
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Ezewudo M, Borens A, Chiner-Oms Á, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J. Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep 2018; 8:15382. [PMID: 30337678 PMCID: PMC6194142 DOI: 10.1038/s41598-018-33731-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022] Open
Abstract
Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
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Affiliation(s)
- Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Amanda Borens
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Álvaro Chiner-Oms
- Joint unit Infection and Public Health FISABIO-CSISP/University of Valencia, Institute of integrative Systems Biology, Valencia, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Leonid Chindelevitch
- School of Computing Science, Simon Fraser University, 8888 University Ave, Burnaby, BC, V5A 1S6, Canada
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA
| | - Debra Hanna
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Richard Liwski
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Matteo Zignol
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Christopher Gilpin
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Borstel, Borstel, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Priority area Infections, Research Center Borstel, Borstel, Germany
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | - Sven Hoffner
- Department of Public Health Sciences, Karolinska institute, Stockholm, Sweden
| | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Street Jaime Roig 11. P.O., 4010, Valencia, Spain
| | - David M Engelthaler
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste 106, Flagstaff, AZ, 86005, USA
| | - David Alland
- Center for Emerging Pathogens, Rutgers-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Leen Rigouts
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christoph Lange
- Division of Clinical Infectious Diseases and German Center for Infection Research Tuberculosis Unit, Research Center Borstel, Borstel, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Ruth McNerney
- Department of Medicine, Division of Pulmonology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA.,The Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA.
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Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microb Genom 2018; 4. [PMID: 30303479 PMCID: PMC6249434 DOI: 10.1099/mgen.0.000217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. tuberculosis outbreaks can be extremely limited - making it difficult to determine precisely who transmitted to whom. In addition to consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) has been proposed to improve resolution. However, few studies have examined the potential biases in detecting these hSNPs. Here, we analysed genome sequence data from 25 specimens from British Columbia, Canada. Specimens were sequenced to a depth of 112-296×. We observed biases in read depth, base quality, strand distribution and read placement where possible hSNPs were initially identified, so we applied conservative filters to reduce false positives. Overall, there was phylogenetic concordance between the observed 2542 cSNP and 63 hSNP loci. Furthermore, we identified hSNPs shared exclusively by epidemiologically linked patients, supporting their use in transmission inferences. We conclude that hSNPs may add resolution to transmission networks, particularly where the overall genetic diversity is low.
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Affiliation(s)
- Michael A Martin
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Robyn S Lee
- 2Department of Epidemiology, Harvard University, Boston, MA 02115, USA
| | - Lauren A Cowley
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jennifer L Gardy
- 3School of Population and Public Health, University of British Columbia, Vancouver, Canada.,4British Columbia Centre for Disease Control, Vancouver, Canada
| | - William P Hanage
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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34
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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: 39] [Impact Index Per Article: 5.6] [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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35
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Ismail N, Omar SV, Ismail NA, Peters RPH. In vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants. J Microbiol Methods 2018; 153:1-9. [PMID: 30165087 DOI: 10.1016/j.mimet.2018.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
Abstract
Bedaquiline, clofazimine and linezolid are pertinent drugs for drug-resistant tuberculosis. Drug-resistant mutants provide insight into important resistance acquisition mechanisms. Methods for in vitro Mycobacterium tuberculosis mutant generation are poorly described. Induction (serial passaging) and spontaneous (adapted Luria-Delbrück assay) approaches using M. tuberculosis ATCC reference strains (one fully-susceptible, four unique mono-resistant) were performed. Mutant MIC values were confirmed (MGIT960) and resultant RAVs compared between approaches and to a catalog of previously published RAVs. Mutant MIC values showed a 3-4-fold (induced) and a 1-4-fold (spontaneous) increase compared to baseline. The pyrazinamide-resistant strain had higher baseline MIC values and acquired resistance (≥4-fold) in fewer passages than other strains (induction approach) for bedaquiline. Previously described and novel RAVs in atpE (8 vs. 1) and rv0678 (4 vs. 12) genes were identified in bedaquiline- and clofazimine-resistant mutants. No rv1979c and rv2535c RAVs were identified. Previously described RAVs were identified in rplC and rrl genes for linezolid-resistant mutants. Both approaches successfully led to in vitro mutants with novel RAVs being described in atpE and rv0678 genes. It was observed that pre-existing resistance may influence mutant phenotypic and genotypic characteristics and warrants further attention.
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Affiliation(s)
- N Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa
| | - S V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - N A Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - R P H Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Department of Medical Microbiology, Maastricht University Medical Centre, School CAPHRI, Care and Public Health Research Institute, Maastricht University, Maastricht, the Netherlands.
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Diagnostic Accuracy and Utility of FluoroType MTBDR, a New Molecular Assay for Multidrug-Resistant Tuberculosis. J Clin Microbiol 2018; 56:JCM.00531-18. [PMID: 29976588 DOI: 10.1128/jcm.00531-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/23/2018] [Indexed: 11/20/2022] Open
Abstract
Most cases of multidrug-resistant (MDR) tuberculosis (TB) are never diagnosed (328,300 of the ∼490,000 cases in 2016 were missed). The Xpert MTB/RIF assay detects resistance only to rifampin, despite ∼20% of rifampin-resistant cases being susceptible to isoniazid (a critical first-line drug). Consequently, many countries require further testing with the GenoType MTBDRplus assay. However, MTBDRplus is not recommended for use on smear-negative specimens, and thus, many specimens require culture-based drug susceptibility testing. Furthermore, MTBDRplus requires specialized expertise, lengthy hands-on time, and significant laboratory infrastructure and interpretation is not automated. To address these gaps, we evaluated the accuracy of the FluoroType MTBDR (FluoroType) assay. Sputa from 244 smear-positive and 204 smear-negative patients with presumptive TB (Xpert MTB positive, n = 343) were tested. Culture and MTBDRplus on isolates served as reference standards (for active TB and MDR-TB, respectively). Sanger sequencing and MTBDRplus, both of which were performed on sputa, were used to resolve discrepancies. The sensitivity of FluoroType for the detection of M. tuberculosis complex was 98% (95% confidence interval [CI], 95 to 99%) and 92% (95% CI, 84 to 96%) for smear-positive and smear-negative specimens, respectively (232/237 versus 90/98 specimens; P < 0.009). The sensitivity and specificity for smear-negative specimens were 100% and 97%, respectively, for rifampin resistance; 100% and 98%, respectively, for isoniazid resistance; and 100% and 100%, respectively, for MDR-TB. FluoroType identified 98%, 97%, and 97% of the rpoB, katG, and inhA promoter mutations, respectively. FluoroType has excellent sensitivity with sputa equivalent to that of MTBDRplus with the isolates and can provide rapid drug susceptibility testing for rifampin and isoniazid. In addition, the capacity of FluoroType to simultaneously identify virtually all mutations in the rpoB, katG, and inhA promoter may be useful for individualized treatment regimens.
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Fitness-compensatory mutations facilitate the spread of drug-resistant F15/LAM4/KZN and F28 Mycobacterium tuberculosis strains in KwaZulu-Natal, South Africa. J Genet 2018; 96:599-612. [PMID: 28947708 DOI: 10.1007/s12041-017-0805-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While the acquisition of drug resistance is often accompanied by fitness costs, Mycobacterium tuberculosis has developed mechanisms to overcome these costs in the form of compensatory mutations. In an attempt to dissect strain-specific differences in biological fitness, 10 M. tuberculosis genomes, representing F15/LAM4/KZN, Beijing, F11 and F28 genotypes were sequenced on the Illumina MiSeq platform. Drug-susceptible F15/LAM4/KZN strains differed by 43 SNPs, demonstrating that heterogeneity exists even among closely-related strains. We found unique, nonsynonymous single-nucleotide polymorphisms (SNPs) in the sigA and grcC1 genes of multidrug resistant (MDR) and XDR F15/LAM4/KZN strains, respectively. The F28 MDR strain harboured a novel ubiA mutation in combination with its embB M306I mutation, which may be related to ethambutol resistance. In addition, it possessed a low-frequency rpoC mutation, suggesting that this strain was in the process of developing compensation. In contrast, no compensatory mutations were identified in Beijing and F11 MDR strains, corroborating its low in vitro fitness. Clinical strains also harboured unique SNPs in a number of important genes associated with virulence, highlighting the need for future studies which examine the correlation of genetic variations with phenotypic diversity. In summary, whole-genome sequencing revealed the presence of fitness-compensatory mutations in F15/LAM4/KZN and F28 genotypes which predominate in MDR and/or extensively drug resistant (XDR) forms in KwaZulu-Natal, South Africa.
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Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis. BMC Genomics 2018; 19:122. [PMID: 29402222 PMCID: PMC5800017 DOI: 10.1186/s12864-018-4498-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/28/2018] [Indexed: 12/03/2022] Open
Abstract
Background Meningitis is the most severe manifestation of tuberculosis. It is largely unknown why some people develop pulmonary TB (PTB) and others TB meningitis (TBM); we examined if the genetic background of infecting M. tuberculosis strains may be relevant. Methods We whole-genome sequenced M. tuberculosis strains isolated from 322 HIV-negative tuberculosis patients from Indonesia and compared isolates from patients with TBM (n = 106) and PTB (n = 216). Using a phylogeny-adjusted genome-wide association method to count homoplasy events we examined phenotype-related changes at specific loci or genes in parallel branches of the phylogenetic tree. Enrichment scores for the TB phenotype were calculated on single nucleotide polymorphism (SNP), gene, and pathway level. Genetic associations were validated in an independent set of isolates. Results Strains belonged to the East-Asian lineage (36.0%), Euro-American lineage (61.5%), and Indo-Oceanic lineage (2.5%). We found no association between lineage and phenotype (Chi-square = 4.556; p = 0.207). Large genomic differences were observed between isolates; the minimum pairwise genetic distance varied from 17 to 689 SNPs. Using the phylogenetic tree, based on 28,544 common variable positions, we selected 54 TBM and 54 PTB isolates in terminal branch sets with distinct phenotypes. Genetic variation in Rv0218, and absence of Rv3343c, and nanK were significantly associated with disease phenotype in these terminal branch sets, and confirmed in the validation set of 214 unpaired isolates. Conclusions Using homoplasy counting we identified genetic variation in three separate genes to be associated with the TB phenotype, including one (Rv0218) which encodes a secreted protein that could play a role in host-pathogen interaction by altering pathogen recognition or acting as virulence effector. Electronic supplementary material The online version of this article (10.1186/s12864-018-4498-z) contains supplementary material, which is available to authorized users.
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Herranz M, Pole I, Ozere I, Chiner-Oms Á, Martínez-Lirola M, Pérez-García F, Gijón P, Serrano MJR, Romero LC, Cuevas O, Comas I, Bouza E, Pérez-Lago L, García-de-Viedma D. Mycobacterium tuberculosis Acquires Limited Genetic Diversity in Prolonged Infections, Reactivations and Transmissions Involving Multiple Hosts. Front Microbiol 2018; 8:2661. [PMID: 29403447 PMCID: PMC5780704 DOI: 10.3389/fmicb.2017.02661] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/20/2017] [Indexed: 01/03/2023] Open
Abstract
Background:Mycobacterium tuberculosis (MTB) has limited ability to acquire variability. Analysis of its microevolution might help us to evaluate the pathways followed to acquire greater infective success. Whole-genome sequencing (WGS) in the analysis of the transmission of MTB has elucidated the magnitude of variability in MTB. Analysis of transmission currently depends on the identification of clusters, according to the threshold of variability (<5 SNPs) between isolates. Objective: We evaluated whether the acquisition of variability in MTB, was more frequent in situations which could favor it, namely intrapatient, prolonged infections or reactivations and interpatient transmissions involving multiple sequential hosts. Methods: We used WGS to analyze the accumulation of variability in sequential isolates from prolonged infections or translations from latency to reactivation. We then measured microevolution in transmission clusters with prolonged transmission time, high number of involved cases, simultaneous involvement of latency and active transmission. Results: Intrapatient and interpatient acquisition of variability was limited, within the ranges expected according to the thresholds of variability proposed, even though bursts of variability were observed. Conclusions: The thresholds of variability proposed for MTB seem to be valid in most circumstances, including those theoretically favoring acquisition of variability. Our data point to multifactorial modulation of microevolution, although further studies are necessary to elucidate the factors underlying this modulation.
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Affiliation(s)
- Marta Herranz
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ilva Pole
- Childhood Tuberculosis Department, Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Riga, Latvia.,Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Ozere
- Childhood Tuberculosis Department, Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Riga, Latvia.,Department of Infectology and Dermatology, Riga Stradinš University, Riga, Latvia
| | - Álvaro Chiner-Oms
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | | | - Felipe Pérez-García
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Paloma Gijón
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María Jesús Ruiz Serrano
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Laura Clotet Romero
- Servei de Vigilància Epidemiològica i Resposta a Emergències de Salut Pública al Vallès Occidental i Vallès Oriental, Subdirecció General de Vigilància i Resposta a Emergències de Salut Pública, Agència de Salut Pública de Catalunya, Barcelona, Spain
| | - Oscar Cuevas
- Servicio de Laboratorio, Institut d'Investigació i Innovació Parc Taulí, I3PT Parc Taulí Hospital Universitari, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Darío García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Jeanes C, O'Grady J. Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution? Int J Mycobacteriol 2018; 5:384-391. [PMID: 27931678 DOI: 10.1016/j.ijmyco.2016.11.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information. These advances mean NGS stands to revolutionise the diagnosis and epidemiological study of Mycobacterium tuberculosis infection. This review focuses on current applications of NGS for TB diagnosis including sequencing cultured isolates to predict drug resistance and, more desirably, direct diagnostic metagenomic sequencing of clinical samples. Also discussed is the potential impact of NGS on the epidemiological study of TB and some of the key challenges that need to be overcome to enable this promising technology to be translated into routine use.
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Affiliation(s)
- Christopher Jeanes
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
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Sekyere JO, Asante J. Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics. Future Microbiol 2018; 13:241-262. [PMID: 29319341 DOI: 10.2217/fmb-2017-0172] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteria and fungi continue to develop new ways to adapt and survive the lethal or biostatic effects of antimicrobials through myriad mechanisms. Novel antibiotic resistance genes such as lsa(C), erm(44), VCC-1, mcr-1, mcr-2, mcr-3, mcr-4, bla KLUC-3 and bla KLUC-4 were discovered through comparative genomics and further functional studies. As well, mutations in genes that hitherto were unknown to confer resistance to antimicrobials, such as trm, PP2C, rpsJ, HSC82, FKS2 and Rv2887, were shown by genomics and transcomplementation assays to mediate antimicrobial resistance in Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, Saccharomyces cerevisae, Candida glabrata and Mycobacterium tuberculosis, respectively. Thus, genomics, transcriptomics and metagenomics, coupled with functional studies are the future of antimicrobial resistance research and novel drug discovery or design.
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Affiliation(s)
- John Osei Sekyere
- Faculty of Pharmacy & Pharmaceutical Sciences, Kwame Nkrumah University of Science & Technology, Kumasi, Ghana
| | - Jonathan Asante
- Faculty of Pharmacy & Pharmaceutical Sciences, Kwame Nkrumah University of Science & Technology, Kumasi, Ghana
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Mortimer TD, Weber AM, Pepperell CS. Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 2018; 3:e00108-17. [PMID: 29404424 PMCID: PMC5790871 DOI: 10.1128/msystems.00108-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.
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Affiliation(s)
- Tatum D. Mortimer
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra M. Weber
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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43
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Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM. Cryptic Microheteroresistance Explains Mycobacterium tuberculosis Phenotypic Resistance. Am J Respir Crit Care Med 2017; 196:1191-1201. [PMID: 28614668 DOI: 10.1164/rccm.201703-0556oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RATIONALE Minority drug-resistant Mycobacterium tuberculosis subpopulations can be associated with phenotypic resistance but are poorly detected by Sanger sequencing or commercial molecular diagnostic assays. OBJECTIVES To determine the role of targeted next-generation sequencing in resolving these minor variant subpopulations. METHODS We used single molecule overlapping reads (SMOR), a targeted next-generation sequencing approach that dramatically reduces sequencing error, to analyze primary cultured isolates phenotypically resistant to rifampin, fluoroquinolones, or aminoglycosides, but for which Sanger sequencing found no resistance-associated variants (RAVs) within respective resistance-determining regions (study group). Isolates also underwent single-colony selection on antibiotic-containing agar, blinded to sequencing results. As a positive control, isolates with multiple colocalizing chromatogram peaks were also analyzed (control group). MEASUREMENTS AND MAIN RESULTS Among 61 primary culture isolates (25 study group and 36 control group), SMOR described 66 (49%) and 45 (33%) of 135 total heteroresistant RAVs at frequencies less than 5% and less than 1% of the total mycobacterial population, respectively. In the study group, SMOR detected minor resistant variant subpopulations in 80% (n = 20/25) of isolates with no Sanger-identified RAVs (median subpopulation size, 1.0%; interquartile range, 0.2-3.9%). Single-colony selection on drug-containing media corroborated SMOR results for 90% (n = 18/20) of RAV-containing specimens, and the absence of RAVs in 60% (n = 3/5) of isolates. Overall, Sanger sequencing was concordant with SMOR for 77% (n = 53/69) of macroheteroresistant (5-95% total population), but only 5% of microheteroresistant (<5%) subpopulations (n = 3/66) across both groups. CONCLUSIONS Cryptic minor variant mycobacterial subpopulations exist below the resolving capability of current drug susceptibility testing methodologies, and may explain an important proportion of false-negative resistance determinations.
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Affiliation(s)
- John Z Metcalfe
- 1 Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, San Francisco, California
| | - Elizabeth Streicher
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Grant Theron
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Rebecca E Colman
- 3 Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, San Diego, California; and
| | | | - Darrin Lemmer
- 4 Translational Genomics Research Institute, Flagstaff, Arizona
| | - Rob Warren
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Heunis T, Dippenaar A, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC, Pain A, Sampson SL, Tabb DL. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates. J Proteome Res 2017; 16:3841-3851. [PMID: 28820946 DOI: 10.1021/acs.jproteome.7b00483] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e., large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.
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Affiliation(s)
- Tiaan Heunis
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Anzaan Dippenaar
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Ruben G van der Merwe
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Nicolaas C Gey van Pittius
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology , Thuwal 23955, Saudi Arabia
| | - Samantha L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
| | - David L Tabb
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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Ramirez-Busby SM, Rodwell TC, Fink L, Catanzaro D, Jackson RL, Pettigrove M, Catanzaro A, Valafar F. A Multinational Analysis of Mutations and Heterogeneity in PZase, RpsA, and PanD Associated with Pyrazinamide Resistance in M/XDR Mycobacterium tuberculosis. Sci Rep 2017; 7:3790. [PMID: 28630430 PMCID: PMC5476565 DOI: 10.1038/s41598-017-03452-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/28/2017] [Indexed: 11/28/2022] Open
Abstract
Pyrazinamide (PZA) is an important first-line drug in all existing and new tuberculosis (TB) treatment regimens. PZA-resistance in M. tuberculosis is increasing, especially among M/XDR cases. Noted issues with PZA Drug Susceptibility Testing (DST) have driven the search for alternative tests. This study provides a comprehensive assessment of PZA molecular diagnostics in M/XDR TB cases. A set of 296, mostly XDR, clinical M. tuberculosis isolates from four countries were subjected to DST for eight drugs, confirmatory Wayne's assay, and whole-genome sequencing. Three genes implicated in PZA resistance, pncA, rpsA, and panD were investigated. Assuming all non-synonymous mutations cause resistance, we report 90% sensitivity and 65% specificity for a pncA-based molecular test. The addition of rpsA and panD potentially provides 2% increase in sensitivity. Molecular heterogeneity in pncA was associated with resistance and should be evaluated as a diagnostic tool. Mutations near the N-terminus and C-terminus of PZase were associated with East-Asian and Euro-American lineages, respectively. Finally, Euro-American isolates are most likely to have a wild-type PZase and escape molecular detection. Overall, the 8-10% resistance without markers may point to alternative mechanisms of resistance. Confirmatory mutagenesis may improve the disconcertingly low specificity but reduce sensitivity since not all mutations may cause resistance.
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Affiliation(s)
- S M Ramirez-Busby
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA
| | - T C Rodwell
- Department of Medicine, University of California, San Diego, California, USA
| | - L Fink
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA
| | - D Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - R L Jackson
- Department of Medicine, University of California, San Diego, California, USA
| | - M Pettigrove
- Department of Medicine, University of California, San Diego, California, USA
| | - A Catanzaro
- Department of Medicine, University of California, San Diego, California, USA
| | - F Valafar
- Biological and Medical Informatics Research Center, San Diego State University, San Diego, California, USA.
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The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome Biol 2017; 18:71. [PMID: 28424085 PMCID: PMC5395877 DOI: 10.1186/s13059-017-1196-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
Background Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. Results By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. Conclusions Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1196-0) contains supplementary material, which is available to authorized users.
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Dippenaar A, Parsons SDC, Miller MA, Hlokwe T, Gey van Pittius NC, Adroub SA, Abdallah AM, Pain A, Warren RM, Michel AL, van Helden PD. Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem. INFECTION GENETICS AND EVOLUTION 2017; 51:235-238. [PMID: 28412523 DOI: 10.1016/j.meegid.2017.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
Abstract
Mycobacterium bovis infects multiple wildlife species and domesticated cattle across South Africa, and negatively impacts on livestock trade and movement of wildlife for conservation purposes. M. bovis infection was first reported in the Kruger National Park (KNP) in South Africa during the 1990s, and has since spread to infect numerous animal host species throughout the park and across South Africa. Whole genome sequencing data of 17 M. bovis isolates were analyzed to investigate the genomic diversity among M. bovis isolates causing disease in different animal host species from various locations in South Africa. M. bovis strains analyzed in this study are geographic rather than host species-specific. The clonal expansion of M. bovis in the KNP highlights the effect of an introduction of a transmissible infectious disease leading to a rising epidemic in wildlife, and emphasizes the importance of disease control and movement restriction of species that serve as disease reservoirs. In conclusion, the point source introduction of a single M. bovis strain type in the KNP ecosystem lead to an M. bovis outbreak in this area that affects various host species and poses an infection risk in neighboring rural communities where HIV prevalence is high.
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Affiliation(s)
- Anzaan Dippenaar
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
| | - Sven David Charles Parsons
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
| | - Michele Ann Miller
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
| | - Tiny Hlokwe
- Tuberculosis Laboratory, ARC-Onderstepoort Veterinary Institute, South Africa.
| | - Nicolaas Claudius Gey van Pittius
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
| | - Sabir Abdu Adroub
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Abdallah Musa Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Robin Mark Warren
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
| | - Anita Luise Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa.
| | - Paul David van Helden
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa.
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Genomic Epidemiology of Tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:79-93. [DOI: 10.1007/978-3-319-64371-7_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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