1
|
Putera I, Ten Berge JCEM, Thiadens AAHJ, Dik WA, Agrawal R, van Hagen PM, La Distia Nora R, Rombach SM. Clinical Features and Predictors of Treatment Outcome in Patients with Ocular Tuberculosis from the Netherlands and Indonesia: The OculaR TB in Low versus High Endemic Countries (ORTEC) Study. Ocul Immunol Inflamm 2024:1-12. [PMID: 38820475 DOI: 10.1080/09273948.2024.2359614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
PURPOSE To describe and compare clinical features, treatment approaches, and treatment outcomes of ocular tuberculosis (OTB) patients in the Netherlands, a low tuberculosis (TB)-endemic country, and Indonesia, a high TB-endemic country. We also aimed to identify predictors of treatment outcomes. METHODS A medical chart review of 339 OTB patients (n = 93 from the Netherlands and n = 246 from Indonesia) was performed. The primary outcome was response to treatment, whether with or without anti-tubercular treatment, after six months of treatment initiation (good versus poor responders). RESULTS Indonesian OTB patients displayed a higher prevalence of chest radiograph findings indicative of TB infection (p < 0.001) and concurrent active systemic TB (p = 0.011). Indonesian cohort exhibited a more acute and severe disease profile, including uveitis duration ≤ 3 months (p < 0.001), blindness (p < 0.001), anterior chamber (AC) cells ≥ 2+ (p < 0.001), and posterior synechiae (p < 0.001). Overall proportions of good responders to treatment were 67.6% in the Netherlands and 71.5% in Indonesia. Presence of AC cell ≥ 2+ (adjusted odds ratio (aOR): 2.12, 95% CI: 1.09-4.14), choroidal lesions other than serpiginous-like choroiditis (SLC) or tuberculoma (aOR: 4.47, 95% CI: 1.18-16.90), and retinal vasculitis (aOR: 2.32, 95% CI: 1.10-4.90) at baseline were predictors for poor response to treatment. CONCLUSIONS Despite a more severe initial clinical presentation in the Indonesian cohort, the overall treatment outcomes of OTB was comparable in both cohorts. Three baseline clinical features were identified as predictors of treatment outcomes.
Collapse
Affiliation(s)
- Ikhwanuliman Putera
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Immunology, Clinical and Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia - Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | | | - Alberta A H J Thiadens
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Willem A Dik
- Department of Immunology, Clinical and Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rupesh Agrawal
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
- Ocular Infections and Antimicrobial Group, Singapore Eye Research Institute, Singapore, Singapore
- National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital, London, UK
| | - P Martin van Hagen
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Immunology, Clinical and Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rina La Distia Nora
- Department of Immunology, Clinical and Laboratory Medical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Faculty of Medicine, Universitas Indonesia - Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Saskia M Rombach
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
2
|
Sadovska D, Ozere I, Pole I, Ķimsis J, Vaivode A, Vīksna A, Norvaiša I, Bogdanova I, Ulanova V, Čapligina V, Bandere D, Ranka R. Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights. Front Public Health 2024; 12:1378426. [PMID: 38832230 PMCID: PMC11144917 DOI: 10.3389/fpubh.2024.1378426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Tuberculosis remains a global health threat, and the World Health Organization reports a limited reduction in disease incidence rates, including both new and relapse cases. Therefore, studies targeting tuberculosis transmission chains and recurrent episodes are crucial for developing the most effective control measures. Herein, multiple tuberculosis clusters were retrospectively investigated by integrating patients' epidemiological and clinical information with median-joining networks recreated based on whole genome sequencing (WGS) data of Mycobacterium tuberculosis isolates. Methods Epidemiologically linked tuberculosis patient clusters were identified during the source case investigation for pediatric tuberculosis patients. Only M. tuberculosis isolate DNA samples with previously determined spoligotypes identical within clusters were subjected to WGS and further median-joining network recreation. Relevant clinical and epidemiological data were obtained from patient medical records. Results We investigated 18 clusters comprising 100 active tuberculosis patients 29 of whom were children at the time of diagnosis; nine patients experienced recurrent episodes. M. tuberculosis isolates of studied clusters belonged to Lineages 2 (sub-lineage 2.2.1) and 4 (sub-lineages 4.3.3, 4.1.2.1, 4.8, and 4.2.1), while sub-lineage 4.3.3 (LAM) was the most abundant. Isolates of six clusters were drug-resistant. Within clusters, the maximum genetic distance between closely related isolates was only 5-11 single nucleotide variants (SNVs). Recreated median-joining networks, integrated with patients' diagnoses, specimen collection dates, sputum smear microscopy, and epidemiological investigation results indicated transmission directions within clusters and long periods of latent infection. It also facilitated the identification of potential infection sources for pediatric patients and recurrent active tuberculosis episodes refuting the reactivation possibility despite the small genetic distance of ≤5 SNVs between isolates. However, unidentified active tuberculosis cases within the cluster, the variable mycobacterial mutation rate in dormant and active states, and low M. tuberculosis genetic variability inferred precise transmission chain delineation. In some cases, heterozygous SNVs with an allelic frequency of 10-73% proved valuable in identifying direct transmission events. Conclusion The complex approach of integrating tuberculosis cluster WGS-data-based median-joining networks with relevant epidemiological and clinical data proved valuable in delineating epidemiologically linked patient transmission chains and deciphering causes of recurrent tuberculosis episodes within clusters.
Collapse
Affiliation(s)
- Darja Sadovska
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Ozere
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Ilva Pole
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Jānis Ķimsis
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Annija Vaivode
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Anda Vīksna
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Inga Norvaiša
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Ineta Bogdanova
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Viktorija Ulanova
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Valentīna Čapligina
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Dace Bandere
- Department of Pharmaceutical Chemistry, Riga Stradiņš University, Riga, Latvia
| | - Renāte Ranka
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| |
Collapse
|
3
|
Valencia-Trujillo D, Avila-Trejo AM, García-Reyes RL, Narváez-Díaz L, Segura del Pilar M, Mújica-Sánchez MA, Becerril-Vargas E, León-Juárez M, Mata-Miranda MM, Rivera-Gutiérrez S, Cerna-Cortés JF. Genetic Diversity of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients in Mexico. Pathogens 2024; 13:428. [PMID: 38787280 PMCID: PMC11124049 DOI: 10.3390/pathogens13050428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.
Collapse
Affiliation(s)
- Daniel Valencia-Trujillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Amanda Marineth Avila-Trejo
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Rocío Liliana García-Reyes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Luis Narváez-Díaz
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mariela Segura del Pilar
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mario Alberto Mújica-Sánchez
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Moises León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México 11000, Mexico;
| | - Mónica Maribel Mata-Miranda
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Jorge Francisco Cerna-Cortés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| |
Collapse
|
4
|
Atavliyeva S, Auganova D, Tarlykov P. Genetic diversity, evolution and drug resistance of Mycobacterium tuberculosis lineage 2. Front Microbiol 2024; 15:1384791. [PMID: 38827149 PMCID: PMC11140050 DOI: 10.3389/fmicb.2024.1384791] [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: 02/12/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024] Open
Abstract
Mycobacterium tuberculosis causes a chronic infectious disease called tuberculosis. Phylogenetic lineage 2 (L2) of M. tuberculosis, also known as the East Asian lineage, is associated with high virulence, increased transmissibility, and the spread of multidrug-resistant strains. This review article examines the genomic characteristics of the M. tuberculosis genome and M. tuberculosis lineage 2, such as the unique insertion sequence and spoligotype patterns, as well as MIRU-VNTR typing, and SNP-based barcoding. The review describes the geographical distribution of lineage 2 and its history of origin. In addition, the article discusses recent studies on drug resistance and compensatory mechanisms of M. tuberculosis lineage 2 and its impact on the pathogen's transmissibility and virulence. This review article discusses the importance of establishing a unified classification for lineage 2 to ensure consistency in terminology and criteria across different studies and settings.
Collapse
Affiliation(s)
- Sabina Atavliyeva
- Genomics and Proteomics Core Facility, National Center for Biotechnology, Astana, Kazakhstan
| | | | - Pavel Tarlykov
- Genomics and Proteomics Core Facility, National Center for Biotechnology, Astana, Kazakhstan
| |
Collapse
|
5
|
Madadi-Goli N, Ahmadi K, Kamakoli MK, Azizi M, Khanipour S, Dizaji SP, Nasehi M, Siadat SD, Fateh A, Vaziri F. The importance of heteroresistance and efflux pumps in bedaquiline-resistant Mycobacterium tuberculosis isolates from Iran. Ann Clin Microbiol Antimicrob 2024; 23:36. [PMID: 38664815 PMCID: PMC11046812 DOI: 10.1186/s12941-024-00694-3] [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: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) continues to pose a threat to communities worldwide and remains a significant public health issue in several countries. We assessed the role of heteroresistance and efflux pumps in bedaquiline (BDQ)-resistant Mycobacterium tuberculosis isolates. METHODS Nineteen clinical isolates were included in the study, of which fifteen isolates were classified as MDR or XDR, while four isolates were fully susceptible. To evaluate BDQ heteroresistance, the Microplate Alamar Blue Assay (MABA) method was employed. For screening mixed infections, MIRU-VNTR was performed on clinical isolates. Mutations in the atpE and Rv0678 genes were determined based on next-generation sequencing data. Additionally, real-time PCR was applied to assess the expression of efflux pump genes in the absence and presence of verapamil (VP). RESULTS All 15 drug-resistant isolates displayed resistance to BDQ. Among the 19 total isolates, 21.05% (4/19) exhibited a heteroresistance pattern to BDQ. None of the isolates carried a mutation of the atpE and Rv0678 genes associated with BDQ resistance. Regarding the MIRU-VNTR analysis, most isolates (94.73%) showed the Beijing genotype. Fifteen (78.9%) isolates showed a significant reduction in BDQ MIC after VP treatment. The efflux pump genes of Rv0676c, Rv1258c, Rv1410c, Rv1634, Rv1819, Rv2459, Rv2846, and Rv3065 were overexpressed in the presence of BDQ. CONCLUSIONS Our results clearly demonstrated the crucial role of heteroresistance and efflux pumps in BDQ resistance. Additionally, we established a direct link between the Rv0676c gene and BDQ resistance. The inclusion of VP significantly reduced the MIC of BDQ in both drug-susceptible and drug-resistant clinical isolates.
Collapse
Affiliation(s)
- Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mahshid Nasehi
- Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
6
|
Ferdosnejad K, Sholeh M, Abdolhamidi R, Soroush E, Siadat SD, Tarashi S. The occurrence rate of Haarlem and Beijing genotypes among Middle Eastern isolates of multi drug resistant Mycobacterium tuberculosis: A systematic review and meta-analysis. Respir Investig 2024; 62:296-304. [PMID: 38295613 DOI: 10.1016/j.resinv.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
Antibiotic resistance is a serious problem that poses a major challenge to tuberculosis control worldwide. Many developing countries still struggle with this infection in term of various aspects as it remains a major health concern. A number of developing countries are located in the Middle East, one of the world's most important regions. The control of this infection remains largely suboptimal despite intensive research in the field, and the mechanisms that lead to its progression have not yet been fully understood. Therefore, TB control must be amended through the identification of new strategies. For this reason, monitoring genetic characterizations of TB strains by molecular typing methods in different geographical regions can be important to setting local programs and global strategies to control TB infection. It is important to know the genotype of Mycobacterium tuberculosis strains to evaluate the occurrence of outbreaks and the transmission of this disease. Beijing and Haarlem genotypes are the most prevalent and, in these families, there is greater association with drug resistance, resulting in more severe forms of TB and higher levels of treatment failure than in other families. The current study is planned to systematically conduct a review using a meta-analysis to show the prevalence of Beijing and Haarlem genotypes in the Middle Eastern MDR-TB cases. M. tuberculosis strains pose particular epidemiological and clinical concerns as they can endanger tuberculosis control programs.
Collapse
Affiliation(s)
| | - Mohammad Sholeh
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Bacteriology, Pasture Institute of Iran, Tehran, Iran
| | | | - Erfan Soroush
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Tarashi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
7
|
Brunner VM, Fowler PW. Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Microb Genom 2024; 10:001187. [PMID: 38315172 PMCID: PMC10926696 DOI: 10.1099/mgen.0.001187] [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: 08/06/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.
Collapse
Affiliation(s)
| | - Philip W. Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| |
Collapse
|
8
|
Abstract
The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.
Collapse
Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
| |
Collapse
|
9
|
Said H, Kachingwe E, Gardee Y, Bhyat Z, Ratabane J, Erasmus L, Lebaka T, van der Meulen M, Gwala T, Omar S, Ismail F, Ismail N. Determining the risk-factors for molecular clustering of drug-resistant tuberculosis in South Africa. BMC Public Health 2023; 23:2329. [PMID: 38001453 PMCID: PMC10668341 DOI: 10.1186/s12889-023-17234-x] [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: 10/05/2022] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (DR-TB) epidemic is driven mainly by the effect of ongoing transmission. In high-burden settings such as South Africa (SA), considerable demographic and geographic heterogeneity in DR-TB transmission exists. Thus, a better understanding of risk-factors for clustering can help to prioritise resources to specifically targeted high-risk groups as well as areas that contribute disproportionately to transmission. METHODS The study analyzed potential risk-factors for recent transmission in SA, using data collected from a sentinel molecular surveillance of DR-TB, by comparing demographic, clinical and epidemiologic characteristics with clustering and cluster sizes. A genotypic cluster was defined as two or more patients having identical patterns by the two genotyping methods used. Clustering was used as a proxy for recent transmission. Descriptive statistics and multinomial logistic regression were used. RESULT The study identified 277 clusters, with cluster size ranging between 2 and 259 cases. The majority (81.6%) of the clusters were small (2-5 cases) with few large (11-25 cases) and very large (≥ 26 cases) clusters identified mainly in Western Cape (WC), Eastern Cape (EC) and Mpumalanga (MP). In a multivariable model, patients in clusters including 11-25 and ≥ 26 individuals were more likely to be infected by Beijing family, have XDR-TB, living in Nelson Mandela Metro in EC or Umgungunglovo in Kwa-Zulu Natal (KZN) provinces, and having history of imprisonment. Individuals belonging in a small genotypic cluster were more likely to infected with Rifampicin resistant TB (RR-TB) and more likely to reside in Frances Baard in Northern Cape (NC). CONCLUSION Sociodemographic, clinical and bacterial risk-factors influenced rate of Mycobacterium tuberculosis (M. tuberculosis) genotypic clustering. Hence, high-risk groups and hotspot areas for clustering in EC, WC, KZN and MP should be prioritized for targeted intervention to prevent ongoing DR-TB transmission.
Collapse
Affiliation(s)
- Halima Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa.
| | - Elizabeth Kachingwe
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Zaheda Bhyat
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - John Ratabane
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Linda Erasmus
- Centre for Enteric Diseases, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Tiisetso Lebaka
- Division of Surveillance and Outbreak Response, National Institute of Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Shaheed Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Farzana Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Moderfontein Road, Sandringham, Johannesburg, code 2131, South Africa
| |
Collapse
|
10
|
Tong E, Zhou Y, Liu Z, Zhu Y, Zhang M, Wu K, Pan J, Jiang J. Bedaquiline Resistance and Molecular Characterization of Rifampicin-Resistant Mycobacterium Tuberculosis Isolates in Zhejiang, China. Infect Drug Resist 2023; 16:6951-6963. [PMID: 37928607 PMCID: PMC10625375 DOI: 10.2147/idr.s429003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Purpose This study aimed to determine the prevalence and molecular characterization of bedaquiline (BDQ) resistance among rifampicin-resistant tuberculosis (RR-TB) isolates collected from Zhejiang, China. Patients and Methods A total of 245 RR-TB isolates were collected from 19 municipal TB hospitals in Zhejiang province, China between January and December 2021. Microplate assays were used to determine the minimum inhibitory concentrations (MIC) of BDQ. Whole-genome sequencing (WGS) was performed on isolates with MIC values for BDQ ≥ 0.25 μg/mL. Results Five (2.04%) BDQ-resistant strains were isolated from 245 tuberculosis patients. The resistance rate of BDQ was not correlated to the sex, age, treatment history, or occupation of patients. Four BDQ-resistant isolates and three BDQ-sensitive isolates were found to carry Rv0678 mutations, and one BDQ-resistant strain carried both Rv0678 and pepQ mutations. No mutations within the atpE and Rv1979c genes were observed. Conclusion BDQ demonstrated strong in vitro antibacterial activity against RR-TB isolates, and the Rv0678 gene was identified as the primary mechanism contributing to BDQ resistance among RR-TB isolates from Zhejiang, China. Furthermore, in addition to the four currently known resistance-associated genes (atpE, Rv0678, Rv1979c, and pepQ), other mechanisms of resistance to BDQ may exist that need further study.
Collapse
Affiliation(s)
- Enyu Tong
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
| | - Ying Zhou
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
| | - Zhengwei Liu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Yelei Zhu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Mingwu Zhang
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Kunyang Wu
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Junhang Pan
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Jianmin Jiang
- School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China
- Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou, 310051, People’s Republic of China
| |
Collapse
|
11
|
Dohál M, Porvazník I, Solovič I, Mokrý J. Advancing tuberculosis management: the role of predictive, preventive, and personalized medicine. Front Microbiol 2023; 14:1225438. [PMID: 37860132 PMCID: PMC10582268 DOI: 10.3389/fmicb.2023.1225438] [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: 05/19/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Tuberculosis is a major global health issue, with approximately 10 million people falling ill and 1.4 million dying yearly. One of the most significant challenges to public health is the emergence of drug-resistant tuberculosis. For the last half-century, treating tuberculosis has adhered to a uniform management strategy in most patients. However, treatment ineffectiveness in some individuals with pulmonary tuberculosis presents a major challenge to the global tuberculosis control initiative. Unfavorable outcomes of tuberculosis treatment (including mortality, treatment failure, loss of follow-up, and unevaluated cases) may result in increased transmission of tuberculosis and the emergence of drug-resistant strains. Treatment failure may occur due to drug-resistant strains, non-adherence to medication, inadequate absorption of drugs, or low-quality healthcare. Identifying the underlying cause and adjusting the treatment accordingly to address treatment failure is important. This is where approaches such as artificial intelligence, genetic screening, and whole genome sequencing can play a critical role. In this review, we suggest a set of particular clinical applications of these approaches, which might have the potential to influence decisions regarding the clinical management of tuberculosis patients.
Collapse
Affiliation(s)
- Matúš Dohál
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University in Ružomberok, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| |
Collapse
|
12
|
Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
Collapse
Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| |
Collapse
|
13
|
Yu J, Liu M, Mijiti X, Liu H, Wang Q, Yin C, Anwaierjiang A, Xu M, Li M, Deng L, Xiao H, Zhao X, Wan K, Li G, Yuan X. Association of Single-Nucleotide Polymorphisms in the VDR Gene with Tuberculosis and Infection of Beijing Genotype Mycobacterium tuberculosis. Infect Drug Resist 2023; 16:3157-3169. [PMID: 37235072 PMCID: PMC10208660 DOI: 10.2147/idr.s407595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Background The aim of the present study was to investigate the association between vitamin D receptor (VDR) gene polymorphism and tuberculosis susceptibility, as well as the potential interaction of host genetic factors with the heterogeneity of Mycobacterium tuberculosis in the population from Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 221 tuberculosis patients as the case group and 363 staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in the VDR were detected by sequencing. M. tuberculosis isolates were collected from the case group and identified as Beijing or non-Beijing lineage by multiplex PCR. Propensity score (PS), univariate analysis and multivariable logistic regression models were used to perform the analysis. Results Our results showed that the allele and genotype frequencies of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in VDR were not correlated with tuberculosis susceptibility or lineages of M. tuberculosis. Two out of six loci of the VDR gene formed one haplotype block, and none of the haplotypes was found to correlate with tuberculosis susceptibility or lineages of M. tuberculosis infected. Conclusion Polymorphisms in the VDR gene may not indicate susceptibility to tuberculosis. There was also no evidence on the interaction between the VDR gene of host and the lineages of M. tuberculosis in the population from Xinjiang, China. Further studies are nonetheless required to prove our conclusions.
Collapse
Affiliation(s)
- Jinjie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | | | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Lele Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
| |
Collapse
|
14
|
Faye LM, Hosu MC, Vasaikar S, Dippenaar A, Oostvogels S, Warren RM, Apalata T. Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa. Pathogens 2023; 12:pathogens12030475. [PMID: 36986397 PMCID: PMC10059723 DOI: 10.3390/pathogens12030475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high-TB-burden country with TB being the highest infectious disease killer. This study investigated the distribution of Mtb mutations and spoligotypes in rural Eastern Cape Province. The Mtb isolates included were 1157 from DR-TB patients and analysed by LPA followed by spoligotyping of 441 isolates. The distribution of mutations and spoligotypes was done by spatial analysis. The rpoB gene had the highest number of mutations. The distribution of rpoB and katG mutations was more prevalent in four healthcare facilities, inhA mutations were more prevalent in three healthcare facilities, and heteroresistant isolates were more prevalent in five healthcare facilities. The Mtb was genetically diverse with Beijing more prevalent and largely distributed. Spatial analysis and mapping of gene mutations and spoligotypes revealed a better picture of distribution.
Collapse
Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Rob M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University and National Health Laboratory Services (NHLS), Private Bag X5117, Mthatha 5099, South Africa
| |
Collapse
|
15
|
Ascher DB, Kaminskas LM, Myung Y, Pires DEV. Using Graph-Based Signatures to Guide Rational Antibody Engineering. Methods Mol Biol 2023; 2552:375-397. [PMID: 36346604 DOI: 10.1007/978-1-0716-2609-2_21] [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] [Indexed: 06/16/2023]
Abstract
Antibodies are essential experimental and diagnostic tools and as biotherapeutics have significantly advanced our ability to treat a range of diseases. With recent innovations in computational tools to guide protein engineering, we can now rationally design better antibodies with improved efficacy, stability, and pharmacokinetics. Here, we describe the use of the mCSM web-based in silico suite, which uses graph-based signatures to rapidly identify the structural and functional consequences of mutations, to guide rational antibody engineering to improve stability, affinity, and specificity.
Collapse
Affiliation(s)
- David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry, Cambridge University, Cambridge, UK
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Lisa M Kaminskas
- School of Biological Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
16
|
Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J. Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 28:100556. [PMID: 36034164 PMCID: PMC9405109 DOI: 10.1016/j.lanwpc.2022.100556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS. METHODS WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number. FINDINGS Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers. INTERPRETATION WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB. FUNDING The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.
Collapse
Affiliation(s)
- Katie Dale
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Victoria, Australia
| | - Simone Bittmann
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Justin Denholm
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
17
|
Soler-Camargo NC, Silva-Pereira TT, Zimpel CK, Camacho MF, Zelanis A, Aono AH, Patané JS, Dos Santos AP, Guimarães AMS. The rate and role of pseudogenes of the Mycobacterium tuberculosis complex. Microb Genom 2022; 8. [PMID: 36250787 DOI: 10.1099/mgen.0.000876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.
Collapse
Affiliation(s)
- Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Maurício F Camacho
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Alexandre H Aono
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil.,Institute of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | | | | | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University
| |
Collapse
|
18
|
Walker TM, Choisy M, Dedicoat M, Drennan PG, Wyllie D, Yang-Turner F, Crook DW, Robinson ER, Walker AS, Smith EG, Peto TE. Mycobacterium tuberculosis transmission in Birmingham, UK, 2009-19: An observational study. THE LANCET REGIONAL HEALTH. EUROPE 2022; 17:100361. [PMID: 35345560 PMCID: PMC8956939 DOI: 10.1016/j.lanepe.2022.100361] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Background Over 10-years of whole-genome sequencing (WGS) of Mycobacterium tuberculosis in Birmingham presents an opportunity to explore epidemiological trends and risk factors for transmission in new detail. Methods Between 1st January 2009 and 15th June 2019, we obtained the first WGS isolate from every patient resident in a postcode district covered by Birmingham's centralised tuberculosis service. Data on patients' sex, country of birth, social risk-factors, anatomical locus of disease, and strain lineage were collected. Poisson harmonic regression was used to assess seasonal variation in case load and a mixed-effects multivariable Cox proportionate hazards model was used to assess risk factors for a future case arising in clusters defined by a 5 single nucleotide polymorphism (SNP) threshold, and by 12 SNPs in a sensitivity analysis. Findings 511/1653 (31%) patients were genomically clustered with another. A seasonal variation in diagnoses was observed, peaking in spring, but only among clustered cases. Risk-factors for a future clustered case included UK-birth (aHR=2·03 (95%CI 1·35-3·04), p < 0·001), infectious (pulmonary/laryngeal/miliary) tuberculosis (aHR=3·08 (95%CI 1·98-4·78), p < 0·001), and M. tuberculosis lineage 3 (aHR=1·91 (95%CI 1·03-3·56), p = 0·041) and 4 (aHR=2·27 (95%CI 1·21-4·26), p = 0·011), vs. lineage 1. Similar results pertained to 12 SNP clusters, for which social risk-factors were also significant (aHR 1·72 (95%CI 1·02-2·93), p = 0·044). There was marked heterogeneity in transmission patterns between postcode districts. Interpretation There is seasonal variation in the diagnosis of genomically clustered, but not non-clustered, cases. Risk factors for clustering include UK-birth, infectious forms of tuberculosis, and infection with lineage 3 or 4. Funding Wellcome Trust, MRC, UKHSA.
Collapse
Affiliation(s)
- Timothy M. Walker
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Marc Choisy
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Martin Dedicoat
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Philip G. Drennan
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, UK
- Oxford University Hospitals NHS Foundation Trust, UK
| | - David Wyllie
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Fan Yang-Turner
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Derrick W. Crook
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Esther R. Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - A. Sarah Walker
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - E. Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Timothy E.A. Peto
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| |
Collapse
|
19
|
Liu M, Wang Q, Liu H, Yin C, Mijiti X, Anwaierjiang A, Wan K, Xu M, Li M, Nong S, Li G, Xiao H. Association of Mannose-Binding Lectin 2 Gene Polymorphism with Tuberculosis Based on Mycobacterium tuberculosis Lineages. Infect Drug Resist 2022; 15:1225-1234. [PMID: 35355619 PMCID: PMC8959721 DOI: 10.2147/idr.s344935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Polymorphisms in MBL2 may contribute to the susceptibility to tuberculosis. The aim of the present study was to determine the associations of the polymorphisms of five loci (rs1800450, rs1800451, rs7096206, rs7095891, and rs11003125) in the MBL2 gene with susceptibility to tuberculosis and specific lineages of Mycobacterium tuberculosis causing tuberculosis in the Uyghur population of Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 170 Uyghur tuberculosis patients as the case group and 147 Uyghur staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of five loci in MBL2 of human were detected by sequencing. Whole-genome sequencing was applied in 68 M. tuberculosis isolates from the case group and the data were used to perform genealogy analysis. Results The distributions of allele and genotype frequencies of five loci in MBL2 varied little between the case and control groups and varied little among the groups, including those infected with different lineages of M. tuberculosis and the control (except those of rs11003125), the P values were all >0.05. The distribution of alleles of rs11003125 was statistically different between patients infected with lineages 3 and 4 M. tuberculosis (χ2=7.037, P=0.008). The C allele and CC genotype of rs11003125 were found to be protective factors against lineage 4 infection when compared to lineage 3 (ORs were 0.190 and 0.158, respectively; 95% confidence intervals were 0.053~0.690 and 0.025~0.999, respectively). Conclusion Our results suggested that human’s susceptibility to tuberculosis is affected both by the host genetic polymorphisms and the lineage of the M. tuberculosis that people were exposed to. However, due to the limitation of the sample size in the present study, larger sample size and more rigorous design should be guaranteed in future studies.
Collapse
Affiliation(s)
- Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Aiketaguli Anwaierjiang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830001, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Siqin Nong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Correspondence: Guilian Li; Hui Xiao, Email ;
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, People’s Republic of China
| |
Collapse
|
20
|
Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [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: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
Collapse
Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| |
Collapse
|
21
|
Zhang Y, Zhao R, Zhang Z, Liu Q, Zhang A, Ren Q, Li S, Long X, Xu H. Analysis of Factors Influencing Multidrug-Resistant Tuberculosis and Validation of Whole-Genome Sequencing in Children with Drug-Resistant Tuberculosis. Infect Drug Resist 2021; 14:4375-4393. [PMID: 34729015 PMCID: PMC8554314 DOI: 10.2147/idr.s331890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022] Open
Abstract
Objective Pediatric tuberculosis (TB) is one of the top ten causes of death in children. Our study was to analyze influencing factors of multidrug-resistant tuberculosis (MDR-TB) and validation of whole-genome sequencing (WGS) used in children with drug-resistant TB (DR-TB). Methods All Mycobacterium tuberculosis (Mtb) strains were isolated from patients aged below 18 years old of Children’s Hospital of Chongqing Medical University, China. A total of 208 Mtb isolates were tested for eight anti-TB drugs with phenotypic drug susceptibility test (DST) and for genetic prediction of the susceptible profile with WGS. The patients corresponding to each strain were grouped according to drug resistance and genotype. Influencing factors of MDR-TB and DR-TB were analyzed. Results According to the phenotypic DST and WGS, 82.2% of Mtb strains were susceptible to all eight drugs, and 6.3% were MDR-TB. Using the phenotypic DSTs as the gold standard, the kappa value of WGS to predict isoniazid, rifampin, ethambutol, rifapentine, prothionamide, levofloxacin, moxifloxacin and amikacin was 0.84, 0.89, 0.59, 0.86, 0.89, 0.82, 0.88 and 1.00, respectively. There was significant difference in the distribution of severe TB, diagnosis, treatment and outcome between MDR and drug-susceptible group (P<0.05). The distribution of severe TB and treatment between DR and drug-susceptible group was statistically different (P<0.05). The results of binary logistic regression showed that Calmette–Guérin bacillus (BCG) vaccine is the protective factor for MDR-TB (OR=0.19), and MDR-TB is the risk factor for PTB and EPTB (OR=17.98). Conclusion The BCG vaccine is a protective factor for MDR-TB, and MDR-TB might not be confined to pulmonary infection, spreading to extrapulmonary organs in children. MDR-TB had more severe cases and a lower recovery rate than drug-susceptible TB. WGS could provide an accurate prediction of drug susceptibility test results for anti-TB drugs, which are needed for the diagnosis and precise treatment of TB in children.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Ruiqiu Zhao
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhenzhen Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Quanbo Liu
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Aihua Zhang
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Qiaoli Ren
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Siyuan Li
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaoru Long
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hongmei Xu
- Department of Infection, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, The Children's Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| |
Collapse
|
22
|
Saati AA, Khurram M, Faidah H, Haseeb A, Iriti M. A Saudi Arabian Public Health Perspective of Tuberculosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10042. [PMID: 34639342 PMCID: PMC8508237 DOI: 10.3390/ijerph181910042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/30/2021] [Accepted: 09/16/2021] [Indexed: 12/02/2022]
Abstract
Tuberculosis is a global health challenge due to its spreading potential. The Kingdom of Saudi Arabia (KSA) faces a challenge in the spread of tuberculosis from migrant workers, but the foremost threat is the huge number of pilgrims who travel to visit sacred sites of the Islamic world located in the holy cities of Makkah and Al Madina. Pilgrims visit throughout the year but especially in the months of Ramadan and Zul-Hijah. The rise of resistance in Mycobacterium tuberculosis is an established global phenomenon that makes such large congregations likely hotspots in the dissemination and spread of disease at a global level. Although very stringent and effective measures exist, the threat remains due to the ever-changing dynamics of this highly pathogenic disease. This overview primarily highlights the current public health challenges posed by this disease to the Saudi health system, which needs to be highlighted not only to the concerned authorities of KSA, but also to the concerned global quarters since the pilgrims and migrants come from all parts of the world with a majority coming from high tuberculosis-burdened countries.
Collapse
Affiliation(s)
- Abdullah A. Saati
- Department of Community Medicine & Pilgrims Healthcare, Faculty of Medicine, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Muhammad Khurram
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al Qura University, Makkah 24382, Saudi Arabia;
| | - Abdul Haseeb
- Department of Clinical Pharmacy, College of Pharmacy, Umm Al Qura University, Makkah 24382, Saudi Arabia;
| | - Marcello Iriti
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- Phytochem Lab, Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, 20133 Milano, Italy
- Center for Studies on Bioispired Agro-Environmental Technology (BAT Center), Università degli Studi di Napoli “Federico II”, 80055 Portici, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
| |
Collapse
|
23
|
Kaewseekhao B, Roytrakul S, Yingchutrakul Y, Laohaviroj M, Salao K, Faksri K. Characterisation of secretome-based immune responses of human leukocytes infected with various Mycobacterium tuberculosis lineages. PeerJ 2021; 9:e11565. [PMID: 34141493 PMCID: PMC8180191 DOI: 10.7717/peerj.11565] [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: 11/26/2020] [Accepted: 05/14/2021] [Indexed: 11/27/2022] Open
Abstract
Background Differences in immune responses against different lineages of Mycobacterium tuberculosis (Mtb), and by different types of immune cell, are still poorly understood. We aimed to compare the secretome-based immune responses among three Mtb lineages and among immune-cell types. The immune responses were also investigated during infection and when the bacilli had been eliminated from the immune cells. Methods Human primary leukocytes were infected with strains representing three lineages of Mtb (East-Asian, Indo-Oceanic and Euro-American). Label-free GeLC MS/MS proteomic analysis of secretomes was performed. The response of each immune-cell type was compared with the appropriate interactome database for each. Results The expression pattern of proteins secreted by Mtb-infected leukocytes differed among Mtb lineages. The ancestral lineage (IO lineage) had a greater ability to activate MMP14 (associated with leukocyte migration) than did the more recent lineages (EA and EuA). During infection, proteins secreted by macrophages, dendritic cells, neutrophils and B-cells were associated with cell proliferation. Following clearance of Mtb, proteins associated with interferon signaling were found in macrophages, dendritic cells and neutrophils: proteins associated with antigen processing were found in B-cells and regulatory T-cells. Expression of immune response-related proteins from many immune-cell types might be suppressed by Mtb infection. Our study has provided a better insight into the host-pathogen interaction and immune response against different Mtb lineages.
Collapse
Affiliation(s)
- Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Marut Laohaviroj
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kanin Salao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| |
Collapse
|
24
|
Said H, Ratabane J, Erasmus L, Gardee Y, Omar S, Dreyer A, Ismail F, Bhyat Z, Lebaka T, van der Meulen M, Gwala T, Adelekan A, Diallo K, Ismail N. Distribution and Clonality of drug-resistant tuberculosis in South Africa. BMC Microbiol 2021; 21:157. [PMID: 34044775 PMCID: PMC8161895 DOI: 10.1186/s12866-021-02232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Background Studies have shown that drug-resistant tuberculosis (DR-TB) in South Africa (SA) is clonal and is caused mostly by transmission. Identifying transmission chains is important in controlling DR-TB. This study reports on the sentinel molecular surveillance data of Rifampicin-Resistant (RR) TB in SA, aiming to describe the RR-TB strain population and the estimated transmission of RR-TB cases. Method RR-TB isolates collected between 2014 and 2018 from eight provinces were genotyped using combination of spoligotyping and 24-loci mycobacterial interspersed repetitive-units-variable-number tandem repeats (MIRU-VNTR) typing. Results Of the 3007 isolates genotyped, 301 clusters were identified. Cluster size ranged between 2 and 270 cases. Most of the clusters (247/301; 82.0%) were small in size (< 5 cases), 12.0% (37/301) were medium sized (5–10 cases), 3.3% (10/301) were large (11–25 cases) and 2.3% (7/301) were very large with 26–270 cases. The Beijing genotype was responsible for majority of RR-TB cases in Western and Eastern Cape, while the East-African-Indian-Somalian (EAI1_SOM) genotype accounted for a third of RR-TB cases in Mpumalanga. The overall proportion of RR-TB cases estimated to be due to transmission was 42%, with the highest transmission-rate in Western Cape (64%) and the lowest in Northern Cape (9%). Conclusion Large clusters contribute to the burden of RR-TB in specific geographic areas such as Western Cape, Eastern Cape and Mpumalanga, highlighting the need for community-wide interventions. Most of the clusters identified in the study were small, suggesting close contact transmission events, emphasizing the importance of contact investigations and infection control as the primary interventions in SA. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02232-z.
Collapse
Affiliation(s)
- Halima Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Department of Medical Microbiology, Faculty of Health Science, University of Free State, Bloemfontein, South Africa.
| | - John Ratabane
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Linda Erasmus
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Shaheed Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | | | - Farzana Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Zaheda Bhyat
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tiisetso Lebaka
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Adeboye Adelekan
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Karidia Diallo
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
25
|
Mudde SE, Alsoud RA, van der Meijden A, Upton AM, Lotlikar MU, Simonsson USH, Bax HI, de Steenwinkel JEM. Predictive modeling to study the treatment-shortening potential of novel tuberculosis drug regimens, towards bundling of preclinical data. J Infect Dis 2021; 225:1876-1885. [PMID: 33606880 PMCID: PMC9159334 DOI: 10.1093/infdis/jiab101] [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] [Received: 11/06/2020] [Accepted: 02/15/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Given the persistently high global burden of tuberculosis (TB), effective and shorter treatment options are needed. Here, we explore the relationship between relapse and treatment length as well as inter-regimen differences for two novel anti-TB drug regimens using a mouse model of TB infection and mathematical modeling. METHODS Mycobacterium tuberculosis-infected mice were treated for up to 13 weeks with bedaquiline and pretomanid combined with moxifloxacin and pyrazinamide (BPaMZ) or linezolid (BPaL). Cure rates were evaluated 12 weeks after treatment completion. The standard regimen of isoniazid, rifampicin, pyrazinamide, and ethambutol (HRZE) was evaluated as a comparator. RESULTS Six weeks of BPaMZ was sufficient to cure all mice. In contrast, 13 weeks of BPaL and 24 weeks of HRZE did not achieve 100% cure rates. Based on mathematical model predictions, 95% probability of cure was predicted for BPaMZ, BPaL and HRZE to occur at 1.6, 4.3, and 7.9 months, respectively. CONCLUSION This study provides additional evidence for the treatment-shortening capacity of BPaMZ over BPaL and HRZE. To optimally utilize preclinical data for predicting clinical outcomes, and to overcome the limitations that hamper such extrapolation, we advocate bundling of available published preclinical data into mathematical models.
Collapse
Affiliation(s)
- Saskia E Mudde
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Rami Ayoun Alsoud
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Aart van der Meijden
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anna M Upton
- Global Alliance for Tuberculosis Drug Development, New York, USA
| | | | | | - Hannelore I Bax
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurriaan E M de Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
26
|
Spoligotype Variation of Mycobacterium tuberculosis Strains Prevailing in Korea. ACTA ACUST UNITED AC 2021; 2020:8874309. [PMID: 33488887 PMCID: PMC7790563 DOI: 10.1155/2020/8874309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/30/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022]
Abstract
Tuberculosis (TB) is an ongoing global health problem, including in South Korea. To manage TB efficiently, it is necessary to understand the epidemiology, transmission route, and characteristics of prevailing Mycobacterium tuberculosis strains. In this study, we investigated microevolutions over time in the spoligotype patterns of M. tuberculosis isolated from TB patients in Korea. We collected 1,055 clinical M. tuberculosis isolates from 16 provinces in Korea from 1994 to 2006 and analyzed them by spoligotyping. We observed 26 subfamilies, including two large predominant families: a Beijing family (72.7%) and the T family (19.1%). Specifically, the abundance of spoligotype SIT269 from the Beijing-like subfamily significantly increased in the 2000s relative to the 1990s in Korea. This study provides an overview of the M. tuberculosis genotype trends over time in Korea. These data also indicate that we should consider the influence of the newly growing SIT269 subtype identified in the Beijing family.
Collapse
|
27
|
Is International Travel an Emerging Issue on Transmission of Beijing Lineage Mycobacterium tuberculosis? J Trop Med 2020; 2020:9357426. [PMID: 32908549 PMCID: PMC7474789 DOI: 10.1155/2020/9357426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/19/2020] [Indexed: 01/29/2023] Open
Abstract
Mycobacterium tuberculosis belonging to Beijing sublineage (BL) is associated with high tuberculosis (TB) transmission, multidrug resistance, and adverse treatment outcomes. Sri Lanka experiences an increase in the number of travellers/workers to and from high TB-burden countries, and there is risk of getting BL strains imported into the country. In this context, a cohort study was conducted to assess the prevalence of BL strains among pulmonary tuberculosis (PTB) patients in the Kandy district of Sri Lanka (a popular tourist destination) and its association with patients' sociodemographic and clinical characteristics. The study population included sputum smear-positive PTB patients diagnosed from February 2018-July 2019. Fresh sputum samples were collected for culturing and conducted polymerase chain reaction using BL-specific primers. Among the 101 patients recruited, presence of BL strains could be ascertained in 94 patients of which 24 (26%; 95% CI: 18%-35%) had BL strains. Prevalence of BL strains was higher among those with high sputum smear grades (2+ and 3+) (P < 0.05) and those who had travelled abroad (P < 0.05). The prevalence was also higher among young people (aged <35 years). Treatment success rates were similar in patients with (83%) and without BL strains (83% vs. 81%; P value = 0.8375). The prevalence of BL strains in Kandy, Sri Lanka, was high compared to previously reported figures in Sri Lanka, and the percentage drives closer to the countries in South East Asia. International travel raises itself as an emerging issue in BL transmission urging the need of policies and practices in immigration/emigration strategies. The study findings have the potential to alter the TB epidemiology in the country and might represent the situation in other underexplored countries as well. Therefore, it is important to monitor the trends and factors related to the prevalence of Beijing strains globally and make decisions as a whole.
Collapse
|
28
|
Pires DEV, Ascher DB. mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. J Chem Inf Model 2020; 60:3450-3456. [PMID: 32615035 DOI: 10.1021/acs.jcim.0c00362] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Development of new potent, safe drugs to treat Mycobacteria has proven to be challenging, with limited hit rates of initial screens restricting subsequent development efforts. Despite significant efforts and the evolution of quantitative structure-activity relationship as well as machine learning-based models for computationally predicting molecule bioactivity, there is an unmet need for efficient and reliable methods for identifying biologically active compounds against Mycobacterium that are also safe for humans. Here we developed mycoCSM, a graph-based signature approach to rapidly identify compounds likely to be active against bacteria from the genus Mycobacterium, or against specific Mycobacteria species. mycoCSM was trained and validated on eight organism-specific and for the first time a general Mycobacteria data set, achieving correlation coefficients of up to 0.89 on cross-validation and 0.88 on independent blind tests, when predicting bioactivity in terms of minimum inhibitory concentration. In addition, we also developed a predictor to identify those compounds likely to penetrate in necrotic tuberculosis foci, which achieved a correlation coefficient of 0.75. Together with a built-in estimator of the maximum tolerated dose in humans, we believe this method will provide a valuable resource to enrich screening libraries with potent, safe molecules. To provide simple guidance in the selection of libraries with favorable anti-Mycobacteria properties, we made mycoCSM freely available online at http://biosig.unimelb.edu.au/myco_csm.
Collapse
Affiliation(s)
- Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne 3004, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville 3052, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville 3052, VIC, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne 3004, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville 3052, VIC, Australia.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
| |
Collapse
|
29
|
Ruhl CR, Pasko BL, Khan HS, Kindt LM, Stamm CE, Franco LH, Hsia CC, Zhou M, Davis CR, Qin T, Gautron L, Burton MD, Mejia GL, Naik DK, Dussor G, Price TJ, Shiloh MU. Mycobacterium tuberculosis Sulfolipid-1 Activates Nociceptive Neurons and Induces Cough. Cell 2020; 181:293-305.e11. [PMID: 32142653 PMCID: PMC7102531 DOI: 10.1016/j.cell.2020.02.026] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/13/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022]
Abstract
Pulmonary tuberculosis, a disease caused by Mycobacterium tuberculosis (Mtb), manifests with a persistent cough as both a primary symptom and mechanism of transmission. The cough reflex can be triggered by nociceptive neurons innervating the lungs, and some bacteria produce neuron-targeting molecules. However, how pulmonary Mtb infection causes cough remains undefined, and whether Mtb produces a neuron-activating, cough-inducing molecule is unknown. Here, we show that an Mtb organic extract activates nociceptive neurons in vitro and identify the Mtb glycolipid sulfolipid-1 (SL-1) as the nociceptive molecule. Mtb organic extracts from mutants lacking SL-1 synthesis cannot activate neurons in vitro or induce cough in a guinea pig model. Finally, Mtb-infected guinea pigs cough in a manner dependent on SL-1 synthesis. Thus, we demonstrate a heretofore unknown molecular mechanism for cough induction by a virulent human pathogen via its production of a complex lipid.
Collapse
Affiliation(s)
- Cody R Ruhl
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Breanna L Pasko
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haaris S Khan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lexy M Kindt
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chelsea E Stamm
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luis H Franco
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Connie C Hsia
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Colton R Davis
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tian Qin
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laurent Gautron
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael D Burton
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA; Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Galo L Mejia
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA; Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Dhananjay K Naik
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA; Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Gregory Dussor
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA; Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Theodore J Price
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX 75080, USA; Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Michael U Shiloh
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|