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Hlanze H, Mutshembele A, Reva ON. Universal Lineage-Independent Markers of Multidrug Resistance in Mycobacterium tuberculosis. Microorganisms 2024; 12:1340. [PMID: 39065108 PMCID: PMC11278869 DOI: 10.3390/microorganisms12071340] [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: 06/18/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: This study was aimed to identify universal genetic markers of multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) and establish statistical associations among identified mutations to enhance understanding of MDR in Mtb and inform diagnostic and treatment development. (2) Methods: GWAS analysis and the statistical evaluation of identified polymorphic sites within protein-coding genes of Mtb were performed. Statistical associations between specific mutations and antibiotic resistance were established using attributable risk statistics. (3) Results: Sixty-four polymorphic sites were identified as universal markers of drug resistance, with forty-seven in PE/PPE regions and seventeen in functional genes. Mutations in genes such as cyp123, fadE36, gidB, and ethA showed significant associations with resistance to various antibiotics. Notably, mutations in cyp123 at codon position 279 were linked to resistance to ten antibiotics. The study highlighted the role of PE/PPE and PE_PGRS genes in Mtb's evolution towards a 'mutator phenotype'. The pathways of acquisition of mutations forming the epistatic landscape of MDR were discussed. (4) Conclusions: This research identifies marker mutations across the Mtb genome associated with MDR. The findings provide new insights into the molecular basis of MDR acquisition in Mtb, aiding in the development of more effective diagnostics and treatments targeting these mutations to combat MDR tuberculosis.
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Affiliation(s)
- Hleliwe Hlanze
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hillcrest, Lynnwood Rd, Pretoria 0002, South Africa;
| | - Awelani Mutshembele
- South African Medical Research Council, TB Platform, 1 Soutpansberg Road, Private Bag X385, Pretoria 0001, South Africa;
| | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hillcrest, Lynnwood Rd, Pretoria 0002, South Africa;
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2
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Holloway-Kew KL, Henneberg M. Dynamics of tuberculosis infection in various populations during the 19th and 20th century: The impact of conservative and pharmaceutical treatments. Tuberculosis (Edinb) 2023; 143S:102389. [PMID: 38012934 DOI: 10.1016/j.tube.2023.102389] [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: 12/11/2022] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 11/29/2023]
Abstract
Humans and Mycobacterium tuberculosis have co-evolved together for thousands of years. Many individuals are infected with the bacterium, but few show signs and symptoms of tuberculosis (TB). Pharmacotherapy to treat those who develop disease is useful, but drug resistance and non-adherence significantly impact the efficacy of these treatments. Prior to the introduction of antibiotic therapies, public health strategies were used to reduce TB mortality. This work shows how these strategies were able to reduce TB mortality in 19th and 20th century populations, compared with antibiotic treatments. Previously published mortality data from historical records for several populations (Switzerland, Germany, England and Wales, Scotland, USA, Japan, Brazil and South Africa) were used. Curvilinear regression was used to examine the reduction in mortality before and after the introduction of antibiotic treatments (1946). A strong decline in TB mortality was already occurring in Switzerland, Germany, England and Wales, Scotland and the USA prior to the introduction of antibiotic treatment. This occurred following many public health interventions including improved sanitation, compulsory reporting of TB cases, diagnostic techniques and sanatoria treatments. Following the introduction of antibiotics, mortality rates declined further, however, this had a smaller effect than the previously employed strategies. In Japan, Brazil and South Africa, reductions in mortality rates were largely driven by antibiotic treatments that caused rapid decline of mortality, with a smaller contribution from public health strategies. For the development of active disease, immune status is important. Individuals infected with the bacterium are more likely to develop signs and symptoms if their immune function is reduced. Effective strategies against TB can therefore include enhancing immune function of the population by improving nutrition, as well as reducing transmission by improving living conditions and public health. This has been effective in the past. Improving immunity may be an important strategy against drug resistant TB.
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Affiliation(s)
- K L Holloway-Kew
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia.
| | - M Henneberg
- Biological Anthropology and Comparative Anatomy Research Unit, School of Biomedicine, University of Adelaide, Australia; Institute of Evolutionary Medicine, University of Zurich, Switzerland.
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3
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Shahin AI, Zaraei SO, Alzuraiqi S, Abdulateef Z, Abbas NE, Al-Tel TH, El-Gamal MI. Evaluation of 2,3-dihydroimidazo[2,1- b]oxazole and imidazo[2,1- b]oxazole derivatives as chemotherapeutic agents. Future Med Chem 2023; 15:1885-1901. [PMID: 37814826 DOI: 10.4155/fmc-2023-0147] [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: 10/11/2023] Open
Abstract
Imidazo[2,1-b]oxazole and 2,3-dihydroimidazo[2,1-b]oxazole ring systems are commonly employed in therapeutically active molecules. In this article, the authors review the utilization of these core scaffolds as chemotherapeutic agents from 2018 to 2022. These scaffolds possess many important biological activities including antimicrobial and anticancer, among others. This review covers their biological activities and structure-activity relationships. One of the most important drugs in this class of compounds is the antitubercular agent delamanid. In this paper, the compounds structure-activity relationship and preclinical and clinical trial data are thoroughly presented.
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Affiliation(s)
- Afnan I Shahin
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shahed Alzuraiqi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Zahaa Abdulateef
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Noora E Abbas
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Taleb H Al-Tel
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
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4
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Zhdanova S, Jiao WW, Sinkov V, Khromova P, Solovieva N, Mushkin A, Mokrousov I, Belopolskaya O, Masharsky A, Vyazovaya A, Rychkova L, Kolesnikova L, Zhuravlev V, Shen AD, Ogarkov O. Insight into Population Structure and Drug Resistance of Pediatric Tuberculosis Strains from China and Russia Gained through Whole-Genome Sequencing. Int J Mol Sci 2023; 24:10302. [PMID: 37373451 DOI: 10.3390/ijms241210302] [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: 05/03/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to determine phenotypic and genotypic drug resistance patterns of Mycobacterium tuberculosis strains from children with tuberculosis (TB) in China and Russia, two high-burden countries for multi/extensively-drug resistant (MDR/XDR) TB. Whole-genome sequencing data of M. tuberculosis isolates from China (n = 137) and Russia (n = 60) were analyzed for phylogenetic markers and drug-resistance mutations, followed by comparison with phenotypic susceptibility data. The Beijing genotype was detected in 126 Chinese and 50 Russian isolates. The Euro-American lineage was detected in 10 Russian and 11 Chinese isolates. In the Russian collection, the Beijing genotype and Beijing B0/W148-cluster were dominated by MDR strains (68% and 94%, respectively). Ninety percent of B0/W148 strains were phenotypically pre-XDR. In the Chinese collection, neither of the Beijing sublineages was associated with MDR/pre-XDR status. MDR was mostly caused by low fitness cost mutations (rpoB S450L, katG S315T, rpsL K43R). Chinese rifampicin-resistant strains demonstrated a higher diversity of resistance mutations than Russian isolates (p = 0.003). The rifampicin and isoniazid resistance compensatory mutations were detected in some MDR strains, but they were not widespread. The molecular mechanisms of M. tuberculosis adaptation to anti-TB treatment are not unique to the pediatric strains, but they reflect the general situation with TB in Russia and China.
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Affiliation(s)
- Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Wei-Wei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Alexander Mushkin
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
- Henan International Joint Laboratory of Children's Infectious Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450012, China
| | - Olesya Belopolskaya
- The Bio-Bank Resource Center, Research Park, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Aleksey Masharsky
- The Bio-Bank Resource Center, Research Park, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
| | - Lubov Rychkova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Lubov Kolesnikova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - A-Dong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Henan International Joint Laboratory of Children's Infectious Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450012, China
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
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5
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Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrob Agents Chemother 2022; 66:e0207521. [PMID: 35532237 DOI: 10.1128/aac.02075-21] [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: 11/20/2022] Open
Abstract
Point mutations in the rrs gene and the eis promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, and 270 AMK-R, CAP-R, and KAN-R isolates, 274 (84.3%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 103 of the phenotypically resistant isolates. A genome-wide association study identified three genes and promoters with mutations that, on aggregate, were associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 5'-untranslated-region mutations with KAN resistance, supporting clinical relevance for this previously demonstrated mechanism of KAN resistance. We also provide evidence for the novel association of CAP resistance with the promoter of the Rv2680-Rv2681 operon, which encodes an exoribonuclease that may influence the binding of CAP to the ribosome. Aggregating mutations by gene can provide additional insight and therefore is recommended for identifying rare mechanisms of resistance when individual mutations carry insufficient statistical power.
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6
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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7
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Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2021; 131:102137. [PMID: 34673379 DOI: 10.1016/j.tube.2021.102137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022]
Abstract
Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.
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8
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Elsaman T, Mohamed MS, Eltayib EM, Abdalla AE, Mohamed MA. Xanthone: A Promising Antimycobacterial Scaffold. Med Chem 2021; 17:310-331. [PMID: 32560609 DOI: 10.2174/1573406416666200619114124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/15/2020] [Accepted: 05/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis (TB) is one of the infectious diseases associated with high rate of morbidity and mortality and still remains one of the top-ten leading causes of human death in the world. The development of new anti-TB drugs is mandatory due to the existence of latent infection as well as the expansion of the resistant Mycobacterium tuberculosis (MBT) strains. Xanthones encompass a wide range of structurally diverse bioactive compounds, obtained either naturally or through chemical synthesis. There is a growing body of literature that recognizes the antitubercular activity of xanthone derivatives. OBJECTIVE The objective of this review is to highlight the main natural sources along with the critical design elements, structure-activity relationships (SARs), modes of action and pharmacokinetic profiles of xanthone-based anti-TB compounds. METHODS In the present review, the anti-TB activity of xanthones reported in the literature from 1972 to date is presented and discussed. RESULTS Exploration of xanthone scaffold led to the identification of several members of this class having superior activity against both sensitive and resistant MBT strains with distinctive mycobacterial membrane disrupting properties. However, studies regarding their modes of action, pharmacokinetic properties and safety are limited. CONCLUSION Comprehendible data and information are afforded by this review and it would certainly provide scientists with new thoughts and means which will be conducive to design and develop new drugs with excellent anti-TB activity through exploration of xanthone scaffold.
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Affiliation(s)
- Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Malik Suliman Mohamed
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Eyman Mohamed Eltayib
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
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Muzondiwa D, Hlanze H, Reva ON. The Epistatic Landscape of Antibiotic Resistance of Different Clades of Mycobacterium tuberculosis. Antibiotics (Basel) 2021; 10:857. [PMID: 34356778 PMCID: PMC8300818 DOI: 10.3390/antibiotics10070857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Drug resistance (DR) remains a global challenge in tuberculosis (TB) control. In order to develop molecular-based diagnostic methods to replace the traditional culture-based diagnostics, there is a need for a thorough understanding of the processes that govern TB drug resistance. The use of whole-genome sequencing coupled with statistical and computational methods has shown great potential in unraveling the complexity of the evolution of DR-TB. In this study, we took an innovative approach that sought to determine nonrandom associations between polymorphic sites in Mycobacterium tuberculosis (Mtb) genomes. Attributable risk statistics were applied to identify the epistatic determinants of DR in different clades of Mtb and the possible evolutionary pathways of DR development. It was found that different lineages of Mtb exploited different evolutionary trajectories towards multidrug resistance and compensatory evolution to reduce the DR-associated fitness cost. Epistasis of DR acquisition is a new area of research that will aid in the better understanding of evolutionary biological processes and allow predicting upcoming multidrug-resistant pathogens before a new outbreak strikes humanity.
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Affiliation(s)
| | | | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (D.M.); (H.H.)
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10
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Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil. Sci Rep 2020; 10:12891. [PMID: 32732910 PMCID: PMC7393130 DOI: 10.1038/s41598-020-69755-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.
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11
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Mokrousov I, Sinkov V, Vyazovaya A, Pasechnik O, Solovieva N, Khromova P, Zhuravlev V, Ogarkov O. Genomic signatures of drug resistance in highly resistant Mycobacterium tuberculosis strains of the early ancient sublineage of Beijing genotype in Russia. Int J Antimicrob Agents 2020; 56:106036. [PMID: 32485278 DOI: 10.1016/j.ijantimicag.2020.106036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 01/09/2023]
Abstract
The Mycobacterium tuberculosis Beijing genotype is a clinically and epidemiologically important lineage that is subdivided into ancient/ancestral and modern strains. In our previous study in western Siberia, we identified variable number of tandem repeats (VNTR)-based clusters within the early ancient sublineage of the Beijing genotype characterized by an unexpectedly high rate of extensive drug resistance (XDR). In the current study, next generation sequencing data were analysed to gain insight into genomic signatures underlying drug resistance of these strains. A total of 184 genomes of the Beijing early ancient sublineage from Russia (16), China (15), Japan (36), Korea (25), Vietnam (18), Thailand (73), and the USA (1) were used for phylogenetic analysis. The drug-resistant profile was deduced genotypically. The Russian isolates were distributed into two clusters and were all drug resistant, mainly pre-XDR and XDR. The largest of these clusters included only Russian isolates from remote locations in both Asian and European parts of the country. All its isolates had a quadruple drug resistance (to isoniazid, rifampin, ethambutol and streptomycin) due to the 6-mutation signature (KatG Ser315Thr, KatG Ile335Val, RpoB Ser450Leu, RpoC Asp485Asn, EmbB Gln497Arg, and RpsL Lys43Arg). In most samples, it was complemented with additional and different pncA, gyrA and rrs mutations leading to the pre-XDR/XDR genotype. Phylogenomic analysis indicates a distant origin of this Russian resistant cluster in the early 1970s but location and circumstances are yet to be clarified.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia.
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia
| | - Oksana Pasechnik
- Department of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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12
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Abstract
The control of tuberculosis (TB) is hampered by the emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis (Mtb) strains, defined as resistant to at least isoniazid and rifampin, the two bactericidal drugs essential for the treatment of the disease. Due to the worldwide estimate of almost half a million incident cases of MDR/rifampin-resistant TB, it is important to continuously update the knowledge on the mechanisms involved in the development of this phenomenon. Clinical, biological and microbiological reasons account for the generation of resistance, including: (i) nonadherence of patients to their therapy, and/or errors of physicians in therapy management, (ii) complexity and poor vascularization of granulomatous lesions, which obstruct drug distribution to some sites, resulting in resistance development, (iii) intrinsic drug resistance of tubercle bacilli, (iv) formation of non-replicating, drug-tolerant bacilli inside the granulomas, (v) development of mutations in Mtb genes, which are the most important molecular mechanisms of resistance. This review provides a comprehensive overview of these issues, and releases up-dated information on the therapeutic strategies recently endorsed and recommended by the World Health Organization to facilitate the clinical and microbiological management of drug-resistant TB at the global level, with attention also to the most recent diagnostic methods.
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13
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Perdigão J, Gomes P, Miranda A, Maltez F, Machado D, Silva C, Phelan JE, Brum L, Campino S, Couto I, Viveiros M, Clark TG, Portugal I. Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. Sci Rep 2020; 10:2600. [PMID: 32054988 PMCID: PMC7018963 DOI: 10.1038/s41598-020-59558-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023] Open
Abstract
Portugal is a low incidence country for tuberculosis (TB) disease. Now figuring among TB low incidence countries, it has since the 1990s reported multidrug resistant and extensively drug resistant (XDR) TB cases, driven predominantly by two strain-types: Lisboa3 and Q1. This study describes the largest characterization of the evolutionary trajectory of M/XDR-TB strains in Portugal, spanning a time-period of two decades. By combining whole-genome sequencing and phenotypic susceptibility data for 207 isolates, we report the geospatial patterns of drug resistant TB, particularly the dispersion of Lisboa3 and Q1 clades, which underly 64.2% and 94.0% of all MDR-TB and XDR-TB isolates, respectively. Genomic-based similarity and a phylogenetic analysis revealed multiple clusters (n = 16) reflecting ongoing and uncontrolled recent transmission of M/XDR-TB, predominantly associated with the Lisboa3 and Q1 clades. These clades are now thought to be evolving in a polycentric mode across multiple geographical districts. The inferred evolutionary history is compatible with MDR- and XDR-TB originating in Portugal in the 70's and 80's, respectively, but with subsequent multiple emergence events of MDR and XDR-TB particularly involving the Lisboa3 clade. A SNP barcode was defined for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed the presence of Lisboa3 and Q1 strains in Europe, South America and Africa. In summary, Portugal displays an unusual and unique epidemiological setting shaped by >40 years of uncontrolled circulation of two main phylogenetic clades, leading to a sympatric evolutionary trajectory towards XDR-TB with the potential for global reach.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
| | - Pedro Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Anabela Miranda
- Departamento de Doenças Infeciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Fernando Maltez
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral, Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Carla Silva
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody E Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | | | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Couto
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Taane G Clark
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
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