1
|
Li YF, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Yu CB, Li HC, Liu Y. Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China. Emerg Microbes Infect 2024; 13:2294858. [PMID: 38126135 PMCID: PMC10866052 DOI: 10.1080/22221751.2023.2294858] [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: 06/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVES We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. METHODS We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. RESULT The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. CONCLUSION MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
Collapse
Affiliation(s)
- Yi-fan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, People’s Republic of China
| | - Xiang-long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, People’s Republic of China
| | - Wan-mei Song
- Department of Respiratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiaotong University, Shanghai, People’s Republic of China
| | - Ya-meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Wei-wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Jie-yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, People’s Republic of China
| | - Huai-chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| |
Collapse
|
2
|
Kumar R, Kolloli A, Singh P, Shi L, Kupz A, Subbian S. The innate memory response of macrophages to Mycobacterium tuberculosis is shaped by the nature of the antigenic stimuli. Microbiol Spectr 2024:e0047324. [PMID: 38980014 DOI: 10.1128/spectrum.00473-24] [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: 02/21/2024] [Accepted: 06/07/2024] [Indexed: 07/10/2024] Open
Abstract
Innate immune cells, such as macrophages, mount an immune response upon exposure to antigens and pathogens. Emerging evidence shows that macrophages exposed to an antigen can generate a "memory-like" response (a.k.a. trained immunity), which confers a non-specific and enhanced response upon subsequent stimulation with a second antigen/microbe. This trained immunity has been implicated in the enhanced response of macrophages against several invading pathogens. However, the association between the nature of the antigen and the corresponding immune correlate of elicited trained immunity is not fully understood. Similarly, the response of macrophages trained and restimulated with homologous stimulants to subsequent infection by pathogenic Mycobacterium tuberculosis (Mtb) remains unexplored. Here, we report the immune and metabolic profiles of trained immunity in human THP-1-derived macrophages after homologous training and restimulation with BCG, LPS, purified protein Derivative (PPD), heat-killed Mtb strains HN878 (hk-HN), and CDC1551 (hk-CDC). Furthermore, the impact of training on the autophagic and antimicrobial responses of macrophages with or without subsequent infection by clinical Mtb isolates HN878 and CDC1551 was evaluated. Results show that repeated stimulation of macrophages with different antigens displays distinct pro-inflammatory, metabolic, antimicrobial, and autophagy induction profiles. These macrophages also induce a differential antimicrobial response upon infection with clinical Mtb HN878 and CDC1551 isolates. A significantly reduced intracellular bacterial load was noted in the stimulated macrophages, which was augmented by the addition of rapamycin, an autophagy inducer. These observations suggest that the nature of the antigen and the mode of stimulation shape the magnitude and breadth of macrophage innate memory response, which impacts subsequent response to Mtb infection. IMPORTANCE Trained immunity (a.k.a. innate memory response) is a novel concept that has been rapidly emerging as a mechanism underpinning the non-specific immunity of innate immune cells, such as macrophages. However, the association between the nature of the stimuli and the corresponding immune correlate of trained immunity is not fully understood. Similarly, the kinetics of immunological and metabolic characteristics of macrophages upon "training" by the same antigen as primary and secondary stimuli (homologous stimulation) are not fully characterized. Furthermore, the ability of antigens such as purified protein derivative (PPD) and heat-killed-Mtb to induce trained immunity remains unknown. Similarly, the response of macrophages primed and trained by homologous stimulants to subsequent infection by pathogenic Mtb is yet to be reported. In this study, we evaluated the hypothesis that the nature of the stimuli impacts the depth and breadth of trained immunity in macrophages, which differentially affects their response to Mtb infection.
Collapse
Affiliation(s)
- Ranjeet Kumar
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Afsal Kolloli
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Pooja Singh
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Lanbo Shi
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Andreas Kupz
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns & Townsville, Queensland, Australia
| | - Selvakumar Subbian
- Public Health Research Institute, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| |
Collapse
|
3
|
Catana-Botello N, Becerril-Montes P, Castro-Garza J, González-Salazar F, Almanza-Reyes H, Del Bosque-Moncayo MDLÁ, Morales-Vargas A, Velázquez-Moreno VM. Mycobacterium tuberculosis Beijing in the State of Nuevo Leon, Mexico. Rev Argent Microbiol 2024:S0325-7541(24)00046-4. [PMID: 38942679 DOI: 10.1016/j.ram.2023.12.007] [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: 05/05/2023] [Revised: 11/16/2023] [Accepted: 12/31/2023] [Indexed: 06/30/2024] Open
Abstract
Tuberculosis remains a serious threat to human health as an infectious disease in Mexico. Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in the State of Nuevo Leon, Mexico are scarce. We aimed to determine the genotypes of circulating MTB belonging to the Beijing lineage recovered from patients in the State of Nuevo Leon, Mexico. A total of 406 MTB isolates from this state were genotyped using the spoligotyping method and 18-locus MIRU-VNTR. Lineage classification and MTB transmission analysis were performed. Based on the spoligotyping analysis, we found 24 strains belonging to the Beijing genotype that were characterized phylogenetically. The MIRUs showed greater discriminatory power than the standard RFLP-IS6110 method; therefore, the greatest allelic diversity among the Beijing strains was observed with MIRU10, MIRU31, MIRU39, MRU40, and MIRU 26. MVLA analysis showed a profile variation between Beijing and non-Beijing strains. The minimum spanning tree (MST) showed that 79% (19) of the strains are related. All Beijing strains exhibited the deletion of region TbD1, which is a characteristic of modern strains. The application of spoligotyping and MIRU-VNTR-18 methods together proved to be more sensitive, discriminatory, and rapid than the standard method for the epidemiological analysis of Mycobacterium Beijing isolates. This study is one of the first to describe the genomic diversity of M. Beijing in the State of Nuevo Leon, Mexico.
Collapse
Affiliation(s)
- Nohemí Catana-Botello
- Faculty of Biological Sciences, Autonomous University of Nuevo León, Ave. Pedro de Alba S/N, Niños Héroes, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León 64260, Mexico
| | - Pola Becerril-Montes
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico.
| | - Jorge Castro-Garza
- Secretary of Health of the State of Nuevo León, C. Mariano Matamoros 520, Nuevo León 64000, Mexico
| | - Francisco González-Salazar
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico; Health Sciences, University of Monterrey, Av. Ignacio Morones Prieto 4500 poniente, Col. Jesús M. Garza, San Pedro Garza García, Nuevo León 66238, Mexico.
| | - Horacio Almanza-Reyes
- Faculty of Medicine and Psychology, Autonomous University of Baja California, Universidad 14418, UABC, Parque Internacional Industrial Tijuana, Tijuana Baja California 22390, Mexico.
| | | | - Alejandro Morales-Vargas
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
| | - Víctor Manuel Velázquez-Moreno
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
| |
Collapse
|
4
|
Bhalla N, Nanda RK. Pangenome-wide association study reveals the selective absence of CRISPR genes (Rv2816c-19c) in drug-resistant Mycobacterium tuberculosis. Microbiol Spectr 2024:e0052724. [PMID: 38916315 DOI: 10.1128/spectrum.00527-24] [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: 02/27/2024] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
The presence of intermittently dispersed insertion sequences and transposases in the Mycobacterium tuberculosis (Mtb) genome makes intra-genome recombination events inevitable. Understanding their effect on the gene repertoires (GR), which may contribute to the development of drug-resistant Mtb, is critical. In this study, publicly available WGS data of clinical Mtb isolates (endemic region n = 2,601; non-endemic region n = 1,130) were de novo assembled, filtered, scaffolded into assemblies, and functionally annotated. Out of 2,601 Mtb WGS data sets from endemic regions, 2,184 (drug resistant/sensitive: 1,386/798) qualified as high quality. We identified 3,784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes in the pangenome of Mtb clinical isolates from endemic regions. Sets of 33 and 39 genes showed positive and negative associations (P < 0.01) with drug resistance status, respectively. Gene ontology clustering showed compromised immunity to phages and impaired DNA repair in drug-resistant Mtb clinical isolates compared to the sensitive ones. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) and CRISPR genes (Rv2816c-19c) were absent in the drug-resistant Mtb. A separate WGS data analysis of drug-resistant Mtb clinical isolates from the Netherlands (n = 1130) also showed the absence of CRISPR genes (Rv2816c-17c). This study highlights the role of CRISPR genes in drug resistance development in Mtb clinical isolates and helps in understanding its evolutionary trajectory and as useful targets for diagnostics development.IMPORTANCEThe results from the present Pan-GWAS study comparing gene sets in drug-resistant and drug-sensitive Mtb clinical isolates revealed intricate presence-absence patterns of genes encoding DNA-binding proteins having gene regulatory as well as DNA modification and DNA repair roles. Apart from the genes with known functions, some uncharacterized and hypothetical genes that seem to have a potential role in drug resistance development in Mtb were identified. We have been able to extrapolate many findings of the present study with the existing literature on the molecular aspects of drug-resistant Mtb, further strengthening the relevance of the results presented in this study.
Collapse
Affiliation(s)
- Nikhil Bhalla
- Translational Health Group, International Center of Genetic Engineering and Biotechnology, New Delhi, India
| | - Ranjan Kumar Nanda
- Translational Health Group, International Center of Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
5
|
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
|
6
|
Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [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: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
Collapse
Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
7
|
Tafess K, Ng TTL, Tam KKG, Leung KSS, Leung JSL, Lee LK, Lao HY, Chan CTM, Yam WC, Wong SSY, Lau TCK, Siu GKH. Genetic mechanisms of co-emergence of INH-resistant Mycobacterium tuberculosis strains during the standard course of antituberculosis therapy. Microbiol Spectr 2024; 12:e0213323. [PMID: 38466098 PMCID: PMC10986572 DOI: 10.1128/spectrum.02133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
The incidence of isoniazid (INH) resistant Mycobacterium tuberculosis is increasing globally. This study aimed to identify the molecular mechanisms behind the development of INH resistance in M. tuberculosis strains collected from the same patients during the standard course of treatment. Three M. tuberculosis strains were collected from a patient before and during antituberculosis (anti-TB) therapy. The strains were characterized using phenotypic drug susceptibility tests, Mycobacterial Interspersed Repeated Unit-Variable-Number Tandem Repeats (MIRU-VNTR), and whole-genome sequencing (WGS) to identify mutations associated with INH resistance. To validate the role of the novel mutations in INH resistance, the mutated katG genes were electroporated into a KatG-deleted M. tuberculosis strain (GA03). Three-dimensional structures of mutated KatG were modeled to predict their impact on INH binding. The pre-treatment strain was susceptible to INH. However, two INH-resistant strains were isolated from the patient after anti-TB therapy. MIRU-VNTR and WGS revealed that the three strains were clonally identical. A missense mutation (P232L) and a nonsense mutation (Q461Stop) were identified in the katG of the two post-treatment strains, respectively. Transformation experiments showed that katG of the pre-treatment strain restored INH susceptibility in GA03, whereas the mutated katG genes from the post-treatment strains rendered negative catalase activity and INH resistance. The protein model indicated that P232L reduced INH-KatG binding affinity while Q461Stop truncated gene transcription. Our results showed that the two katG mutations, P232L and Q461Stop, accounted for the co-emergence of INH-resistant clones during anti-TB therapy. The inclusion of these mutations in the design of molecular assays could increase the diagnostic performance.IMPORTANCEThe evolution of drug-resistant strains of Mycobacterium tuberculosis within the lung lesions of a patient has a detrimental impact on treatment outcomes. This is particularly concerning for isoniazid (INH), which is the most potent first-line antimycobacterial drug. However, the precise genetic factors responsible for drug resistance in patients have not been fully elucidated, with approximately 15% of INH-resistant strains harboring unknown genetic factors. This raises concerns about the emergence of drug-resistant clones within patients, further contributing to the global epidemic of resistance. In this study, we revealed the presence of two novel katG mutations, which emerged independently due to the stress exerted by antituberculosis (anti-TB) treatment on a parental strain. Importantly, we experimentally demonstrated the functional significance of both mutations in conferring resistance to INH. Overall, this research sheds light on the genetic mechanisms underlying the evolution of INH resistance within patients and provides valuable insights for improving diagnostic performance by targeting specific mutations.
Collapse
Affiliation(s)
- Ketema Tafess
- Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Samson Sai Yin Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Terrence Chi-Kwong Lau
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| |
Collapse
|
8
|
Lan Y, Crudu V, Ciobanu N, Codreanu A, Chitwood MH, Sobkowiak B, Warren JL, Cohen T. Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model. EBioMedicine 2024; 102:105085. [PMID: 38531172 PMCID: PMC10987885 DOI: 10.1016/j.ebiom.2024.105085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Multidrug resistant tuberculosis (MDR-TB) represents a major public health concern in the Republic of Moldova, with an estimated 31% of new and 56% of previously treated TB cases having MDR disease in 2022. A recent genomic epidemiology study of incident TB occurring in 2018 and 2019 found that 92% of MDR-TB was the result of transmission. The MDR phenotype was concentrated among two M. tuberculosis (Mtb) lineages: L2.2.1 (Beijing) and L4.2.1 (Ural). METHODS We developed and applied a hierarchical Bayesian multinominal logistic regression model to Mtb genomic, spatial, and epidemiological data collected from all individuals with diagnosed TB in Moldova in 2018 and 2019 to identify locations in which specific Mtb strains are being transmitted. We then used a logistic regression model to estimate locality-level factors associated with local transmission. FINDINGS We found differences in the spatial distribution and degree of local concentration of disease due to specific strains of Beijing and Ural lineage Mtb. Foci of transmission for four strains of Beijing lineage Mtb, predominantly of the MDR-TB phenotype, were located in several regions, but largely concentrated in Transnistria. In contrast, transmission of Ural lineage Mtb had less marked patterns of spatial aggregation, with a single strain (also of the MDR phenotype) spatially clustered in southern Transnistria. We found a 30% (95% credible interval 2%-80%) increase in odds of a locality being a transmission cluster for each increase of 100 persons per square kilometer, while higher local tuberculosis incidence and poverty were not associated with a locality being a transmission focus. INTERPRETATION Our results identified localities where specific Mtb transmission networks were concentrated and quantified the association between locality-level factors and focal transmission. This analysis revealed Transnistria as the primary area where specific Mtb strains (predominantly of the MDR-TB phenotype) were locally transmitted and suggests that targeted intensified case finding in this region may be an attractive policy option. FUNDING Funding for this work was provided by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.
Collapse
Affiliation(s)
- Yu Lan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | | | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| |
Collapse
|
9
|
Rudeeaneksin J, Bunchoo S, Phetsuksiri B, Srisungngam S, Khummin R, Thapa J, Nakajima C, Suzuki Y. The first insight into Mycobacterium tuberculosis complex isolates in the lower northern region in Thailand. Trans R Soc Trop Med Hyg 2024:trae014. [PMID: 38554067 DOI: 10.1093/trstmh/trae014] [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: 11/19/2023] [Revised: 01/21/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains an important infectious disease and different genotypes have been reported. This study aimed to investigate the genetic diversity and molecular epidemiology of TB in the lower northern region of Thailand, where genotyping data are limited. METHODS A total of 159 Mycobacterium tuberculosis complex (MTBC) isolates from this region were genotyped by spoligotyping and the major spoligotypes were further subdivided by the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. RESULTS Spoligotyping identified 34 types and classified them into 14 clusters. East African-Indian (EAI) groups were the most frequent (44.7%), followed by Beijing (36.5%), with a higher prevalence of drug resistance. By 15-loci MIRU-VNTR typing, the major groups of the Beijing and EAI2_NTB were further differentiated into 44 and 21 subtypes forming 9 and 5 subclusters with cluster rates of 0.26 and 0.44, respectively. The Hunter-Gaston Discriminatory Index among the Beijing and EAI2_NTB groups were 0.987 and 0.931, respectively, indicating high diversity. CONCLUSIONS This is the first look at the MTBC genotypes in the lower northern region of Thailand, which could aid in understanding the distribution and potential spread of MTBC and Mycobacterium bovis in the target region to support TB control in Thailand.
Collapse
Affiliation(s)
- Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
- Medical Sciences Technical Office, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Ratchaneeporn Khummin
- Office of Disease Prevention and Control Region 2 Phitsanulok, Department of Disease Control, Ministry of Public Health, Phitsanulok 65000, Thailand
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| |
Collapse
|
10
|
Dheda K, Mirzayev F, Cirillo DM, Udwadia Z, Dooley KE, Chang KC, Omar SV, Reuter A, Perumal T, Horsburgh CR, Murray M, Lange C. Multidrug-resistant tuberculosis. Nat Rev Dis Primers 2024; 10:22. [PMID: 38523140 DOI: 10.1038/s41572-024-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Tuberculosis (TB) remains the foremost cause of death by an infectious disease globally. Multidrug-resistant or rifampicin-resistant TB (MDR/RR-TB; resistance to rifampicin and isoniazid, or rifampicin alone) is a burgeoning public health challenge in several parts of the world, and especially Eastern Europe, Russia, Asia and sub-Saharan Africa. Pre-extensively drug-resistant TB (pre-XDR-TB) refers to MDR/RR-TB that is also resistant to a fluoroquinolone, and extensively drug-resistant TB (XDR-TB) isolates are additionally resistant to other key drugs such as bedaquiline and/or linezolid. Collectively, these subgroups are referred to as drug-resistant TB (DR-TB). All forms of DR-TB can be as transmissible as rifampicin-susceptible TB; however, it is more difficult to diagnose, is associated with higher mortality and morbidity, and higher rates of post-TB lung damage. The various forms of DR-TB often consume >50% of national TB budgets despite comprising <5-10% of the total TB case-load. The past decade has seen a dramatic change in the DR-TB treatment landscape with the introduction of new diagnostics and therapeutic agents. However, there is limited guidance on understanding and managing various aspects of this complex entity, including the pathogenesis, transmission, diagnosis, management and prevention of MDR-TB and XDR-TB, especially at the primary care physician level.
Collapse
Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fuad Mirzayev
- Global Tuberculosis Programme, WHO, Geneva, Switzerland
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital & Research Center, Mumbai, India
| | - Kelly E Dooley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kwok-Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong, SAR, China
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anja Reuter
- Sentinel Project on Paediatric Drug-Resistant Tuberculosis, Boston, MA, USA
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Megan Murray
- Department of Epidemiology, Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Paediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| |
Collapse
|
11
|
Blankson HNA, Kamara RF, Barilar I, Andres S, Conteh OS, Dallenga T, Foray L, Maurer F, Kranzer K, Utpatel C, Niemann S. Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone. Microbiol Spectr 2024; 12:e0240523. [PMID: 38289066 PMCID: PMC10923214 DOI: 10.1128/spectrum.02405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 03/06/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) management has become a serious global health challenge. Understanding its epidemic determinants on the regional level is crucial for developing effective control measures. We used whole genome sequencing data of 238 of Mycobacterium tuberculosis complex (MTBC) strains to determine drug resistance profiles, phylogeny, and transmission dynamics of MDR/rifampicin-resistant (RR) MTBC strains from Sierra Leone. Forty-two strains were classified as RR, 196 as MDR, 5 were resistant to bedaquiline (BDQ) and clofazimine (CFZ), but none was found to be resistant to fluoroquinolones. Sixty-one (26%) strains were resistant to all first-line drugs, three of which had additional resistance to BDQ/CFZ. The strains were classified into six major MTBC lineages (L), with strains of L4 being the most prevalent, 62% (n = 147), followed by L6 (Mycobacterium africanum) strains, (21%, n = 50). The overall clustering rate (using ≤d12 single-nucleotide polymorphism threshold) was 44%, stratified into 31 clusters ranging from 2 to 16 strains. The largest cluster (n = 16) was formed by sublineage 2.2.1 Beijing Ancestral 3 strains, which developed MDR several times. Meanwhile, 10 of the L6 strains had a primary MDR transmission. We observed a high diversity of drug resistance mutations, including borderline resistance mutations to isoniazid and rifampicin, and mutations were not detected by commercial assays. In conclusion, one in five strains investigated was resistant to all first-line drugs, three of which had evidence of BDQ/CFZ resistance. Implementation of interventions such as rapid diagnostics that prevent further resistance development and stop MDR-TB transmission chains in the country is urgently needed. IMPORTANCE A substantial proportion of MDR-TB strains in Sierra Leone were resistant against all first line drugs; however this makes the all-oral-six-month BPaLM regimen or other 6-9 months all oral regimens still viable, mainly because there was no FQ resistance.Resistance to BDQ was detected, as well as RR, due to mutations outside of the hotspot region. While the prevalence of those resistances was low, it is still cause for concern and needs to be closely monitored.
Collapse
Affiliation(s)
- Harriet N. A. Blankson
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - Rashidatu Fouad Kamara
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Ousman S. Conteh
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Tobias Dallenga
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- Cellular Microbiology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Lynda Foray
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Florian Maurer
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| |
Collapse
|
12
|
Li YF, Yang Y, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Men D, Yu CB, Yang GR, Han WG, Liu WY, Yan K, Li HC, Liu Y. Transmission dynamics and phylogeography of Mycobacterium tuberculosis in China based on whole-genome phylogenetic analysis. Int J Infect Dis 2024; 140:124-131. [PMID: 37863309 DOI: 10.1016/j.ijid.2023.10.015] [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: 05/12/2023] [Revised: 09/30/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
OBJECTIVES This study aimed to describe the lineage-specific transmissibility and epidemiological migration of Mycobacterium tuberculosis in China. METHODS We curated a large set of whole-genome sequences from 3204 M. tuberculosis isolates, including thousands of newly sequenced genomes, and applied a series of metrics to compare the transmissibility of M. tuberculosis strains between lineages and sublineages. The countrywide transmission patterns of major lineages were explored. RESULTS We found that lineage 2 (L2) was the most prevalent lineage in China (85.7%), with the major sublineage 2.2.1 (80.9%), followed by lineage 4 (L4) (13.8%), which comprises major sublineages 4.2 (1.5%), 4.4 (6.2%) and 4.5 (5.8%). We showed evidence for frequent cross-regional spread and large cluster formation of L2.2.1 strains, whereas L4 strains were relatively geographically restricted in China. Next, we applied a series of genomic indices to evaluate M. tuberculosis strain transmissibility and uncovered higher transmissibility of L2.2.1 compared with the L2.2.2 and L4 sublineages. Phylogeographic analysis showed that southern, eastern, and northern China were highly connected regions for countrywide L2.2.1 strain spread. CONCLUSIONS The present study provides insights into the different transmission and migration patterns of the major M. tuberculosis lineages in China and highlights that transmissible L2.2.1 is a threat to tuberculosis control.
Collapse
Affiliation(s)
- Yi-Fan Li
- Department of Respiratory and Critical Care Medicine, the Third Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, PR China
| | - Yang Yang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao, PR China
| | - Xiang-Long Kong
- Xiang-long Kong, Shandong Artificial Intelligence Institute Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Wan-Mei Song
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China; Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Dan Men
- College of Geography and Environmental Science, Northwest Normal University, No. 967 Anning East Road, Lanzhou, Gansu Province, China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, Shandong, PR China
| | - Guo-Ru Yang
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Ge Han
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Wen-Yu Liu
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Kun Yan
- Department of Respiratory and Critical Care Medicine, Weifang Respiratory Disease Hospital & Weifang No. 2 People's Hospital, Weifang, Shandong, PR China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, PR China.
| |
Collapse
|
13
|
Barilar I, Fernando T, Utpatel C, Abujate C, Madeira CM, José B, Mutaquiha C, Kranzer K, Niemann T, Ismael N, de Araujo L, Wirth T, Niemann S, Viegas S. Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study. THE LANCET. INFECTIOUS DISEASES 2024; 24:297-307. [PMID: 37956677 DOI: 10.1016/s1473-3099(23)00498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND In 2021, an estimated 4800 people developed rifampicin-resistant tuberculosis in Mozambique, 75% of which went undiagnosed. Detailed molecular data on rifampicin-resistant and multidrug-resistant (MDR) tuberculosis are not available. Here, we aimed at gaining precise data on the determinants of rifampicin-resistant and MDR tuberculosis in Mozambique. METHODS In this retrospective observational study, we performed whole-genome sequencing of 704 rifampicin-resistant Mycobacterium tuberculosis complex (Mtbc) strains submitted to the National Tuberculosis Reference Laboratory (NTRL) in Maputo, Mozambique, between 2015 and 2021. Phylogenetic strain classification, genomic resistance prediction, and cluster analysis were performed. FINDINGS Between Jan 1, 2015, and July 31, 2021, 2606 Mtbc isolates with an isoniazid or rifampicin resistance were identified in the NTRL biobank, of which, 1483 (56·9%) were from men, 1114 (42·7%) from women, and nine (0·4%) were unknown. Genome-based drug-resistant prediction classified 704 Mtbc strains as rifampicin resistant. 628 (89%) of the 704 Mtbc strains were classified MDR; of those, 146 (23%) were pre-extensively drug resistant (pre-XDR; additional fluoroquinolone resistance), and 24 (4%) extensively drug resistant (XDR; combined fluoroquinolone and bedaquiline resistance). Overall, 61 (9%) of 704 strains revealed resistance to bedaquiline: five (7%) of 76 rifampicin resistant plus bedaquiline resistant, 32 (7%) of 458 MDR plus bedaquiline resistant, and 24 (100%) of 24 XDR. Prevalence of bedaquiline resistance increased from 3% in 2016 to 14% in 2021. The cluster rate (12 single-nucleotide polymorphism threshold) was 42% for rifampicin-resistant strains, 78% for MDR strains, 94% for pre-XDR strains, and 96% for XDR Mtbc strains. 31 (4%) of 704 Mtbc strains, belonging to a diagnostic escape outbreak strain previously described in Eswatini (group_56), had an rpoB Ile491Phe mutation which is not detected by Xpert MTB/RIF (no other rpoB mutation). Of these, 23 (74%) showed additional resistance to bedaquiline, 13 (42%) had bedaquiline and fluoroquinolone resistance, and two (6%) were bedaquiline, fluoroquinolone, and delamanid resistant. INTERPRETATION Pre-XDR resistance is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance; and the frequency of bedaquiline resistance quadrupled over time and was found even in Mtbc strains without fluoroquinolone resistance. Importantly, strains with Ile491Phe mutation were frequent, accounting for 31% (n=10) of MDR plus bedaquiline-resistant strains and 54% (n=13) of XDR Mtbc strains. Given the current diagnostic algorithms and treatment regimens, both the emergence of rifampicin resistance due to Ile491Phe and bedaquiline resistance might jeopardise MDR tuberculosis prevention and care unless sequencing-based technology is rolled out. The potential cross border spread of diagnostic escape strains needs further investigation. FUNDING The German Ministry of Health through the Seq_MDRTB-Net project, the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy Precision Medicine in Inflammation and the Research Training Group 2501 TransEvo, the Leibniz Science Campus Evolutionary Medicine of the Lung, and the German Ministry of Education and Research via the German Center for Infection Research.
Collapse
Affiliation(s)
- Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | | | - Benedita José
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Claudia Mutaquiha
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Katharina Kranzer
- Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität, Munich, Munich, Germany
| | - Tanja Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Nalia Ismael
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thierry Wirth
- Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres University, Paris, France; Institut de Systématique, Evolution, Biodiversite, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France; Ecole Pratique des Hautes Etudes, Université des Antilles, Paris, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia.
| | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene, Mozambique
| |
Collapse
|
14
|
Utpatel C, Zavaleta M, Rojas-Bolivar D, Mühlbach A, Picoy J, Portugal W, Esteve-Solé A, Alsina L, Miotto P, Bartholomeu DC, Sanchez J, Cuadros DF, Alarcon JO, Niemann S, Huaman MA. Prison as a driver of recent transmissions of multidrug-resistant tuberculosis in Callao, Peru: a cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2024; 31:100674. [PMID: 38500964 PMCID: PMC10945431 DOI: 10.1016/j.lana.2024.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 03/20/2024]
Abstract
Background We sought to identify resistance patterns and key drivers of recent multidrug-resistant tuberculosis (MDR-TB) transmission in a TB-prevalent area in Peru. Methods Cross-sectional study including MDR Mycobacterium tuberculosis complex (Mtbc) strains identified in Callao-Peru between April 2017 and February 2019. Mtbc DNA was extracted for whole genome sequencing which was used for phylogenetic inference, clustering, and resistance mutation analyses. Clusters indicative of recent transmission were defined based on a strain-to-strain distance of ≤5 (D5) single nucleotide polymorphisms (SNPs). Epidemiologic factors linked to MDR-TB clustering were analyzed using Poisson regression. Findings 171 unique MDR-Mtbc strains were included; 22 (13%) had additional fluoroquinolone resistance and were classified as pre-XDR. Six strains (3.5%) harboured bedaquiline (BDQ) resistance mutations and were classified as MDR + BDQ. 158 (92%) Mtbc strains belonged to lineage 4 and 13 (8%) to lineage 2. Using a cluster threshold of ≤5 SNPs, 98 (57%) strains were grouped in one of the 17 D5 clusters indicative of recent transmission, ranging in size from 2 to the largest cluster formed by 53 4.3.3 strains (group_1). Lineage 4.3.3 strains showed the overall highest cluster rate (43%). In multivariate analyses, current or previous imprisonment was independently associated with being part of any MDR-TB transmission clusters (adjusted prevalence ratio [aPR], 1.45; 95% CI, 1.09-1.92). Interpretation Pre-XDR-TB emerged in more than 10% of the MDR-TB strains investigated. Transmission of 4.3.3 Mtbc strains especially of the dominant group_1 clone is a major driver of the MDR-TB epidemic in Callao. Current or previous imprisonment was linked to recent MDR-TB transmissions, indicating an important role of prisons in driving the MDR-TB epidemic. Funding This work was supported in part by the ERANet-LAC Network of the European Union, Latin America and the Caribbean Countries on Joint Innovation and Research Activities, and FONDECYT. Additional support was received from Leibniz Science Campus Evolutionary Medicine of the Lung, the Deutsche Forschungsgemeinschaft (German Research Foundation, under Germany's Excellence Strategy-EXC 2167 Precision Medicine in Inflammation), and the Research Training Group 2501 TransEvo.
Collapse
Affiliation(s)
- Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Milagros Zavaleta
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Daniel Rojas-Bolivar
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Andreas Mühlbach
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Janet Picoy
- Direccion Regional de Salud del Callao, Callao, Peru
| | | | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu Institut de Recerca Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu Institut de Recerca Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniella C. Bartholomeu
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
| | - Diego F. Cuadros
- Department of Geography and GIS, Health Geography and Disease Modeling Laboratory, University of Cincinnati, Cincinnati, USA
| | - Jorge O. Alarcon
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
- Epidemiology Section, Instituto de Medicina Tropical, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Moises A. Huaman
- Centro de Investigaciones Tecnológicas, Biomedicas y Medioambientales, Callao, Peru
- Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati, Cincinnati, USA
| |
Collapse
|
15
|
Dohál M, Dvořáková V, Šperková M, Pinková M, Ghodousi A, Omrani M, Porvazník I, Rasmussen EM, Škereňová M, Krivošová M, Wallenfels J, Konstantynovska O, Walker TM, Nikolayevskyy V, Cirillo DM, Solovič I, Mokrý J. Tuberculosis in Ukrainian War Refugees and Migrants in the Czech Republic and Slovakia: A Molecular Epidemiological Study. J Epidemiol Glob Health 2024; 14:35-44. [PMID: 38048026 PMCID: PMC11043285 DOI: 10.1007/s44197-023-00166-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND The war in Ukraine has led to significant migration to neighboring countries, raising public health concerns. Notable tuberculosis (TB) incidence rates in Ukraine emphasize the immediate requirement to prioritize approaches that interrupt the spread and prevent new infections. METHODS We conducted a prospective genomic surveillance study to assess migration's impact on TB epidemiology in the Czech Republic and Slovakia. Mycobacterium tuberculosis isolates from Ukrainian war refugees and migrants, collected from September 2021 to December 2022 were analyzed alongside 1574 isolates obtained from Ukraine, the Czech Republic, and Slovakia. RESULTS Our study revealed alarming results, with historically the highest number of Ukrainian tuberculosis patients detected in the host countries. The increasing number of cases of multidrug-resistant TB, significantly linked with Beijing lineage 2.2.1 (p < 0.0001), also presents substantial obstacles to control endeavors. The genomic analysis identified the three highly related genomic clusters, indicating the recent TB transmission among migrant populations. The largest clusters comprised war refugees diagnosed in the Czech Republic, TB patients from various regions of Ukraine, and incarcerated individuals diagnosed with pulmonary TB specialized facility in the Kharkiv region, Ukraine, pointing to a national transmission sequence that has persisted for over 14 years. CONCLUSIONS The data showed that most infections were likely the result of reactivation of latent disease or exposure to TB before migration rather than recent transmission occurring within the host country. However, close monitoring, appropriate treatment, careful surveillance, and social support are crucial in mitigating future risks, though there is currently no evidence of local transmission in EU countries.
Collapse
Affiliation(s)
- Matúš Dohál
- Comenius University Bratislava, Malá Hora 4A, 036 01, Martin, Slovak Republic.
| | - Věra Dvořáková
- National Institute of Public Health, Prague, Czech Republic
| | | | | | - Arash Ghodousi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele University, Milan, Italy
- University of Milan, Milan, Italy
| | - Maryam Omrani
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovak Republic
- Catholic University, Ružomberok, Slovak Republic
| | | | - Mária Škereňová
- Comenius University Bratislava, Malá Hora 4A, 036 01, Martin, Slovak Republic
| | - Michaela Krivošová
- Comenius University Bratislava, Malá Hora 4A, 036 01, Martin, Slovak Republic
| | | | | | - Timothy M Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- University of Oxford, Oxford, UK
| | | | | | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovak Republic
- Catholic University, Ružomberok, Slovak Republic
| | - Juraj Mokrý
- Comenius University Bratislava, Malá Hora 4A, 036 01, Martin, Slovak Republic
| |
Collapse
|
16
|
Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
Collapse
Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| |
Collapse
|
17
|
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
|
18
|
Dreyer V, Sonnenkalb L, Diricks M, Utpatel C, Barilar I, Mohr V, Niemann S, Kohl TA, Merker M. Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles. Methods Mol Biol 2024; 2833:195-210. [PMID: 38949712 DOI: 10.1007/978-1-0716-3981-8_18] [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: 07/02/2024]
Abstract
Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and susceptibility for many first- and second-line anti-tuberculosis drugs. However, bioinformatic pipelines and mutation catalogs to predict antimicrobial resistances in MTBC isolates are often customized and detailed protocols are difficult to access. Here, we provide a step-by-step workflow for the processing and interpretation of short-read sequencing data and give an overview of available analysis pipelines.
Collapse
Affiliation(s)
- Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Vanessa Mohr
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
| |
Collapse
|
19
|
Akhmetova A, Bismilda V, Chingissova L, Filipenko M, Akilzhanova A, Kozhamkulov U. Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan. Antibiotics (Basel) 2023; 13:9. [PMID: 38275319 PMCID: PMC10812519 DOI: 10.3390/antibiotics13010009] [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: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis was additionally performed for the Beijing isolates. The identification of mutations in the drug-resistance genes of M. tuberculosis was performed with allele-specific real-time PCR and Sanger sequencing. The Beijing genotype was identified in 60% (324/540) of the clinical isolates. Central Asian/Russian cluster 94-32 was the most distributed cluster among the Beijing isolates (50.3%; 163/324). Three other dominant Beijing clusters were identified as 94-33 (3.4%; 11/324), 100-32 (3.1%; 10/324) and 99-32 (3.1%; 10/324). The Beijing genotype was associated with drug-resistant TB (p < 0.0001), including multidrug-resistant TB (p < 0.0001), in our study. An association of the mutation Ser531Leu of the rpoB gene with the Beijing genotype was found (p < 0.0001; OR = 16.0000; 95%CI: 4.9161-52.0740). Among the Beijing isolates, cluster 94-32 showed an association with MDR-TB (p = 0.021). This is why the evaluation of the Beijing genotype and its clusters is needed to control MDR-TB in Kazakhstan.
Collapse
Affiliation(s)
- Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Astana 010000, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Maxim Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630000, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| |
Collapse
|
20
|
Ogwang MO, Diero L, Ng'ong'a F, Magoma G, Mutharia L, Imbuga M, Ngugi C. Strain structure analysis of Mycobacterium tuberculosis circulating among HIV negative, positive and drug resistant TB patients attending chest clinics in Western Kenya. BMC Pulm Med 2023; 23:497. [PMID: 38071287 PMCID: PMC10709907 DOI: 10.1186/s12890-023-02802-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Despite global tuberculosis (TB) interventions, the disease remains one of the major public health concerns. Kenya is ranked 15th among 22 high burden TB countries globally. METHODS A cross-sectional study was conducted in Western Kenya, which comprises 10 counties. A multistage sampling method was used where a single sub-county was randomly selected followed by sampling two high volume health facility from each sub-county. Identification of spoligotype profiles and their family distribution and lineage level were achieved by comparison with SITVIT database. RESULTS Lineage distribution pattern revealed that the most predominant lineage was CAS 220 (39.8%) followed by Beijing 128 (23.1%). The other lineages identified were T, LAM, H, X, S and MANU which were quantified as 87 (15.7%), 67 (12.1%), 16 (2.8%), 10 (1.8%), 8 (1.4%) and 5 (0.9%) respectively. CAS and Beijing strains were the most predominant lineage in both HIV negative and positive TB patients. The Beijing lineage was also the most predominant in resistant M. tuberculosis strains as compared to wild type. A total of 12 (2.0%) were orphaned M. tuberculosis strains which were spread across all the 10 counties of the study site. In multivariate logistic regression adjusting for potential cofounders three potential risk factors were significant. HIV status (OR = 1.52, CI = 0.29-3.68 and P value of 0.001), Alcohol use (OR = 0.59, CI = 0.43-3.12 and P-value =0.001) and cross border travel (OR = 0.61, CI = 0.49-3.87 and P value = 0.026). Most M. tuberculosis clinical isolates showed genetic clustering with multivariate logistic regression indicating three potential risk factors to clustering. HIV status (OR = 1.52, CI = 0.29-3.68 and P value of 0.001), Alcohol use (OR = 0.59, CI = 0.43-3.12 and P-value =0.001) and cross border travel (OR = 0.61, CI = 0.49-3.87 and P value = 0.026). CONCLUSION There exist diverse strains of M. tuberculosis across the 10 counties of Western Kenya. Predominant distribution of clustered genotype points to the fact that most TB cases in this region are as a result of resent transmission other than activation of latent TB.
Collapse
Affiliation(s)
- Martin O Ogwang
- School of Public Health Nairobi Kenya, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.
| | - Lameck Diero
- School of Medicine, Moi University, Eldoret, Kenya
| | - Florence Ng'ong'a
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Gabriel Magoma
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Lucy Mutharia
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, ON, Canada
| | - Mabel Imbuga
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Caroline Ngugi
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| |
Collapse
|
21
|
Senelle G, Sahal MR, La K, Billard-Pomares T, Marin J, Mougari F, Bridier-Nahmias A, Carbonnelle E, Cambau E, Refrégier G, Guyeux C, Sola C. Towards the reconstruction of a global TB history using a new pipeline "TB-Annotator". Tuberculosis (Edinb) 2023; 143S:102376. [PMID: 38012933 DOI: 10.1016/j.tube.2023.102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 11/29/2023]
Abstract
Mycobacterium tuberculosis complex (MTBC) has a population structure consisting of 9 human and animal lineages. The genomic diversity within these lineages is a pathogenesis factor that affects virulence, transmissibility, host response, and antibiotic resistance. Hence it is important to develop improved information systems for tracking and understanding the spreading and evolution of genomes. We present results obtained thanks to a new informatics platform for computational biology of MTBC, that uses a convenience sample from public/private SRAs, designated as TB-Annotator. Version 1 was a first interactive graphic-based web tool based on 15,901 representative genomes. Version 2, still interactive, is a more sophisticated database, developed using the Snakemake Workflow Management System (WMS) that allows an unsupervised global and scalable analysis of the content of the USA National Center for Biotechnology Information Short Read Archives database. This platform analyzes nucleotide variants, the presence/absence of genes, known regions of difference and detect new deletions, the insertion sites of mobile genetic elements, and allows phylogenetic trees to be built, imported in a graphical interface and interactively analyzed between the data and the tree. The objective of TB-Annotator is triple: detect recent epidemiological links, reconstruct distant phylogeographical histories as well as perform more complex phenotypic/genotypic Genome-Wide Association Studies (GWAS). In this paper, we compare the various taxonomic SNPs-based labels and hierarchies previously described in recent reference papers for L1, and present a comparative analysis that allows identification of alias and thus provides the basis of a future unifying naming scheme for L1 sublineages. We present a global phylogenetic tree built with RAxML-NG, and one on L2; at the time of writing, we characterized about 200 sublineages, with many new ones; a detail tree for Modern L2 and a hierarchical scheme allowing to facilitate L2 lineage assignment are also presented.
Collapse
Affiliation(s)
- Gaetan Senelle
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Muhammed Rabiu Sahal
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France
| | - Kevin La
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Typhaine Billard-Pomares
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Julie Marin
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Faiza Mougari
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | | | - Etienne Carbonnelle
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Emmanuelle Cambau
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Guislaine Refrégier
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Christophe Sola
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France.
| |
Collapse
|
22
|
Chesov E, Chesov D, Reimann M, Dreyer V, Utpatel C, Gröschel MI, Ciobanu N, Crudu V, Lange C, Heyckendorf J, Merker M. Impact of Mycobacterium tuberculosis strain type on multidrug-resistant tuberculosis severity, Republic of Moldova. J Infect 2023; 87:588-591. [PMID: 37827458 DOI: 10.1016/j.jinf.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Affiliation(s)
- Elena Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova; Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany
| | - Dumitru Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova; Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany
| | - Maja Reimann
- Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Germany
| | - Viola Dreyer
- German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charite ́ - Universitaetsmedizin Berlin, Berlin, Germany
| | - Nelly Ciobanu
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Christoph Lange
- Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Germany; Baylor College of Medicine and Texas Children´s Hospital, Houston, TX, USA
| | - Jan Heyckendorf
- Clinic for Internal Medicine I, University Clinic Schleswig-Holstein Campus Kiel, Germany
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
| |
Collapse
|
23
|
Mekonnen D, Munshea A, Nibret E, Adnew B, Getachew H, Kebede A, Gebrewahid A, Herrera-Leon S, Aramendia AA, Benito A, Abascal E, Jacqueline C, Aseffa A, Herrera-Leon L. Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020-2022: In-silico Whole-Genome Sequence Analysis. Infect Drug Resist 2023; 16:6859-6870. [PMID: 37908783 PMCID: PMC10614653 DOI: 10.2147/idr.s429001] [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: 07/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020-2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.
Collapse
Affiliation(s)
- Daniel Mekonnen
- Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshea
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | | | | | - Amiro Kebede
- Amhara Public Health Institute, Bahir Dar, Ethiopia
| | | | - Silvia Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain
| | - Estefanía Abascal
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Jacqueline
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Laura Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
| |
Collapse
|
24
|
Losev Y, Rubinstein M, Nissan I, Haviv P, Barsky Y, Volinsky M, Bar-Giora G, Zouher T, Hamawi M, Valenci GZ, Kutikov I, Shwartz HK, Dveyrin Z, Chemtob D, Rorman E. Genomic, phenotypic and demographic characterization of Mycobacterium tuberculosis in Israel in 2021. Front Cell Infect Microbiol 2023; 13:1196904. [PMID: 37928179 PMCID: PMC10622789 DOI: 10.3389/fcimb.2023.1196904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
According to World Health Organization WHO, Tuberculosis (TB) is the second cause of death from infectious disease worldwide. During 2021, 10.6 million people were infected with TB, and 1.6 million people died. TB is caused by pathogens belonging to the Mycobacterium tuberculosis complex (MTBC), mainly by Mycobacterium tuberculosis (M.tb). Members of this complex are acid-fast bacilli, which can cause intrapulmonary and extra pulmonary TB, and can be divided into various lineages, based on genomic markers. The main public health threat comes from drug resistant M.tb strains, which are responsible for about 25% of TB death and treatment failure worldwide. Treating drug resistant TB patients significantly raises the costs of TB treatment. This study provides an overview of the demographic and drug susceptibility characteristics of newly diagnosed TB patients in Israel in 2021. The State of Israel has a very low level of TB endemicity and is at a pre-elimination phase. Notably, only 11.7% of the newly diagnosed TB patients were born in Israel. In this report, of the 154 new laboratory-confirmed TB patients, 66.7% had pulmonary TB, while 16% had extrapulmonary TB. Males accounted for 52% of the patients, with the most prevalent age group being 21-40. Most patients were citizens of Israel (53.9%), while 37.7% had no Israeli citizenship. Among non-citizens, there was a predominance of males and patients aged 21-40. The susceptibility profile showed a high resistance rate to streptomycin (18.2%) and to a lower extent to isoniazid (13.6%), pyrazinamide (8.4%), rifampicin (7.8%), and ethambutol (3.2%). Only 2 cases of XDR-TB and 10 MDR-TB strains were detected in Israel in 2021, with both XDR strains and 5 out of 10 MDR strains belonging to the Beijing lineage. Most of Beijing isolates were resistant to at least one tested drug. Genomic sequencing of 134 out of 156 strains and bioinformatics analysis using the MTBseq program and WHO mutation catalogue shows a good match with only 9 discrepancies between phenotypic and genotypic susceptibility profiles in first line drugs. The most common lineage is Delhi-Cas (23%) followed by the Beijing lineage (17%). Most patients from the Delhi-Cas lineage were born in Africa, while patients with Beijing isolates were born in different countries. Minimum spanning tree analysis identified 15 clusters. The study highlights the need for ongoing surveillance of TB using molecular and phenotypic tools to further decreasing the spreading level of the disease and develop effective treatment strategies.
Collapse
Affiliation(s)
- Yelena Losev
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Mor Rubinstein
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Paz Haviv
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yohi Barsky
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Martha Volinsky
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gefen Bar-Giora
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Tamara Zouher
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Mazal Hamawi
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Ina Kutikov
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Hasia Kaidar Shwartz
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Daniel Chemtob
- Department of Tuberculosis (TB) and AIDS and National TB Program Manager, Ministry of Health, Jerusalem, Israel
- Hebrew University-Hadassah Faculty of Medicine, School of Public Health and Community Medicine, Jerusalem, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| |
Collapse
|
25
|
Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
Collapse
Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| |
Collapse
|
26
|
Auganova D, Atavliyeva S, Amirgazin A, Akisheva A, Tsepke A, Tarlykov P. Genomic Characterization of Drug-Resistant Mycobacterium tuberculosis L2/Beijing Isolates from Astana, Kazakhstan. Antibiotics (Basel) 2023; 12:1523. [PMID: 37887224 PMCID: PMC10604462 DOI: 10.3390/antibiotics12101523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Kazakhstan ranks among the countries with the highest number of MDR-TB patients per 100,000 population worldwide. The successful transmission of local MDR strains of Mycobacterium tuberculosis (Mtb) poses a significant threat to disease control. In this study, we employed whole-genome sequencing to examine drug resistance, compensatory mutations, population structure, and transmission patterns in a sample of 24 clinical isolates of L2/Beijing Mtb collected in Astana, Kazakhstan between 2021 and 2022. The genotypic prediction of Mtb susceptibility to anti-TB agents was consistent with the phenotypic susceptibility, except for bedaquiline. An analysis of resistance-associated genes characterized most of the isolates as pre-extensively drug-resistant tuberculosis (pre-XDR-TB) (n = 15; 62.5%). The phylogenetic analysis grouped the isolates into four transmission clusters; the dominant cluster was assigned to the "aggressive" Central Asia outbreak (CAO) clade of L2/Beijing (n = 15; 62.5%). Thirteen mutations with putative compensatory effects were observed exclusively in Mtb isolates containing the rpoB S450L mutation. The putative compensatory mutations had a stabilizing effect on RpoABC protein stability and dynamics. The high prevalence of the CAO clade in the population structure of Mtb may explain the rapid spread of MDR-TB in Kazakhstan.
Collapse
Affiliation(s)
- Dana Auganova
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
| | | | | | - Akmaral Akisheva
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Anna Tsepke
- City Center for Phthisiopulmonology of the Akimat of Astana, Astana 010000, Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan (A.A.)
| |
Collapse
|
27
|
Vīksna A, Sadovska D, Berge I, Bogdanova I, Vaivode A, Freimane L, Norvaiša I, Ozere I, Ranka R. Genotypic and phenotypic comparison of drug resistance profiles of clinical multidrug-resistant Mycobacterium tuberculosis isolates using whole genome sequencing in Latvia. BMC Infect Dis 2023; 23:638. [PMID: 37770850 PMCID: PMC10540372 DOI: 10.1186/s12879-023-08629-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) remains a major public health problem in many high tuberculosis (TB) burden countries. Phenotypic drug susceptibility testing (DST) take several weeks or months to result, but line probe assays and Xpert/Rif Ultra assay detect a limited number of resistance conferring gene mutations. Whole genome sequencing (WGS) is an advanced molecular testing method which theoretically can predict the resistance of M. tuberculosis (Mtb) isolates to all anti-TB agents through a single analysis. METHODS Here, we aimed to identify the level of concordance between the phenotypic and WGS-based genotypic drug susceptibility (DS) patterns of MDR-TB isolates. Overall, data for 12 anti-TB medications were analyzed. RESULTS In total, 63 MDR-TB Mtb isolates were included in the analysis, representing 27.4% of the total number of MDR-TB cases in Latvia in 2012-2014. Among them, five different sublineages were detected, and 2.2.1 (Beijing group) and 4.3.3 (Latin American-Mediterranean group) were the most abundant. There were 100% agreement between phenotypic and genotypic DS pattern for isoniazid, rifampicin, and linezolid. High concordance rate (> 90%) between phenotypic and genotypic DST results was detected for ofloxacin (93.7%), pyrazinamide (93.7%) and streptomycin (95.4%). Phenotypic and genotypic DS patterns were poorly correlated for ethionamide (agreement 56.4%), ethambutol (85.7%), amikacin (82.5%), capreomycin (81.0%), kanamycin (85.4%), and moxifloxacin (77.8%). For capreomycin, resistance conferring mutations were not identified in several phenotypically resistant isolates, and, in contrary, for ethionamide, ethambutol, amikacin, kanamycin, and moxifloxacin the resistance-related mutations were identified in several phenotypically sensitive isolates. CONCLUSIONS WGS is a valuable tool for rapid genotypic DST for all anti-TB agents. For isoniazid and rifampicin phenotypic DST potentially can be replaced by genotypic DST based on 100% agreement between the tests. However, discrepant results for other anti-TB agents limit their prescription based solely on WGS data. For clinical decision, at the current level of knowledge, there is a need for combination of genotypic DST with modern, validated phenotypic DST methodologies for those medications which did not showed 100% agreement between the methods.
Collapse
Affiliation(s)
- Anda Vīksna
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
- Rīga Stradiņš University, Riga, Latvia
| | - Darja Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Iveta Berge
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Ineta Bogdanova
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Annija Vaivode
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Lauma Freimane
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia
| | - Inga Norvaiša
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
| | - Iveta Ozere
- Riga East Clinical University Hospital, Centre of Tuberculosis and Lung Diseases, Ropaži Municipality, Stopiņi Parish, Upeslejas, Latvia
- Rīga Stradiņš University, Riga, Latvia
| | - Renāte Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, Riga, LV-1067, Latvia.
| |
Collapse
|
28
|
Friedman SR, Smyrnov P, Vasylyeva TI. Will the Russian war in Ukraine unleash larger epidemics of HIV, TB and associated conditions and diseases in Ukraine? Harm Reduct J 2023; 20:119. [PMID: 37658448 PMCID: PMC10472698 DOI: 10.1186/s12954-023-00855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
The Russian war in Ukraine poses many risks for the spread of HIV, TB and associated conditions, including possible increases in the numbers of people who inject drugs or engage in sex work in the years ahead. Ukrainian civil society and volunteer efforts have been able to maintain and at times expand services for HIV Key Populations. The extent of mutual-aid and volunteer efforts as well as the continued strength and vitality of harm reduction organizations such as the Alliance for Public Health and the rest of civil society will be crucial resources for postwar efforts to assist Key Populations and prevent the spread of HIV, TB and other diseases. The postwar period will pose great economic and political difficulties for Ukrainians, including large populations of people physically and/or psychically damaged and in pain who might become people who inject drugs. Local and international support for public health and for harm reduction will be needed to prevent potentially large-scale increases in infectious disease and related mortality.
Collapse
Affiliation(s)
| | | | - Tetyana I Vasylyeva
- Division of Infectious Diseases and Global Public Health, UC San Diego, San Diego, CA, USA.
| |
Collapse
|
29
|
Berry SB, Espich S, Thuong NTT, Chang X, Dorajoo R, Khor CC, Heng CK, Yuan JM, Fox D, Anaya-Sanchez A, Tenney L, Chang CJ, Kotov DI, Vance RE, Dunstan SJ, Darwin KH, Stanley SA. Disruption of Aldehyde Dehydrogenase 2 protects against bacterial infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554661. [PMID: 37662190 PMCID: PMC10473740 DOI: 10.1101/2023.08.24.554661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ALDH2*2 (rs671) allele is one of the most common genetic mutations in humans, yet the positive evolutionary selective pressure to maintain this mutation is unknown, despite its association with adverse health outcomes. ALDH2 is responsible for the detoxification of metabolically produced aldehydes, including lipid-peroxidation end products derived from inflammation. Here, we demonstrate that host-derived aldehydes 4-hydroxynonenal (4HNE), malondialdehyde (MDA), and formaldehyde (FA), all of which are metabolized by ALDH2, are directly toxic to the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis at physiological levels. We find that Aldh2 expression in macrophages is decreased upon immune stimulation, and that bone marrow-derived macrophages from Aldh2 -/- mice contain elevated aldehydes relative to wild-type mice. Macrophages deficient for Aldh2 exhibited enhanced control of Francisella infection. Finally , mice lacking Aldh2 demonstrated increased resistance to pulmonary infection by M. tuberculosis , including in a hypersusceptible model of tuberculosis, and were also resistant to Francisella infection. We hypothesize that the absence of ALDH2 contributes to the host's ability to control infection by pathogens such as M. tuberculosis and F. tularensis , and that host-derived aldehydes act as antimicrobial factors during intracellular bacterial infections. One sentence summary Aldehydes produced by host cells contribute to the control of bacterial infections.
Collapse
|
30
|
Zhu C, Yang T, Yin J, Jiang H, Takiff HE, Gao Q, Liu Q, Li W. The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains. Microbiol Spectr 2023; 11:e0333922. [PMID: 37272796 PMCID: PMC10434187 DOI: 10.1128/spectrum.03339-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/23/2023] [Indexed: 06/06/2023] Open
Abstract
Strains of the Mycobacterium tuberculosis complex (MTBC) Beijing family aroused concern because they were often found in clusters and appeared to be exceptionally transmissible. However, it was later found that strains of the Beijing family were heterogeneous, and the transmission advantage was restricted to sublineage L2.3 or modern Beijing. In this study, we analyzed the previously published genome sequences of 7,896 L2.3 strains from 51 different countries. Using BEAST software to approximate the temporal emergence of L2.3, our calculations suggest that L2.3 initially emerged in northern East Asia during the early 15th century and subsequently diverged into six phylogenetic clades, identified as L2.3.1 through L2.3.6. Using terminal branch length and genomic clustering as proxies for transmissibility, we found that the six clades displayed distinct population dynamics, with the three recently emerged clades (L2.3.4 to L2.3.6) exhibiting significantly higher transmissibility than the older three clades (L2.3.1 to L2.3.3). Of the Beijing family strains isolated outside East Asia, 83.1% belonged to the clades L2.3.4 to L2.3.6, which were also associated with more cross-border transmission. This work reveals the heterogeneity in sublineage L2.3 and demonstrates that the global success of Beijing family strains is driven by the three recently emerged L2.3 clades. IMPORTANCE The recent population dynamics of the global tuberculosis epidemic are heavily shaped by Mycobacterium tuberculosis complex (MTBC) strains with enhanced transmissibility. The infamous Beijing family strain stands out because it has rapidly spread throughout the world. Identifying the strains responsible for the global expansion and tracing their evolution should help to understand the nature of high transmissibility and develop effective strategies to control transmission. In this study, we found that the L2.3 sublineage diversified into six phylogenetic clades (L2.3.1 to L2.3.6) with various transmission characteristics. Clades L2.3.4 to L2.3.6 exhibited significantly higher transmissibility than clades L2.3.1 to L2.3.3, which helps explain why more than 80% of Beijing family strains collected outside East Asia belong to these three clades. We conclude that the global success of L2.3 was not caused by the entire L2.3 sublineage but rather was due to the rapid expansion of L2.3.4 to L2.3.6. Tracking the transmission of L2.3.4 to L2.3.6 strains can help to formulate targeted TB prevention and control.
Collapse
Affiliation(s)
- Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | | | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Científicas, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| |
Collapse
|
31
|
Rollo RF, Mori G, Hill TA, Hillemann D, Niemann S, Homolka S, Fairlie DP, Blumenthal A. Wollamide Cyclic Hexapeptides Synergize with Established and New Tuberculosis Antibiotics in Targeting Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0046523. [PMID: 37289062 PMCID: PMC10433873 DOI: 10.1128/spectrum.00465-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 06/09/2023] Open
Abstract
Shorter and more effective treatment regimens as well as new drugs are urgent priorities for reducing the immense global burden of tuberculosis (TB). As treatment of TB currently requires multiple antibiotics with diverse mechanisms of action, any new drug lead requires assessment of potential interactions with existing TB antibiotics. We previously described the discovery of wollamides, a new class of Streptomyces-derived cyclic hexapeptides with antimycobacterial activity. To further assess the value of the wollamide pharmacophore as an antimycobacterial lead, we determined wollamide interactions with first- and second-line TB antibiotics by determining fractional inhibitory combination index and zero interaction potency scores. In vitro two-way and multiway interaction analyses revealed that wollamide B1 synergizes with ethambutol, pretomanid, delamanid, and para-aminosalicylic acid in inhibiting the replication and promoting the killing of phylogenetically diverse clinical and reference strains of the Mycobacterium tuberculosis complex (MTBC). Wollamide B1 antimycobacterial activity was not compromised in multi- and extensively drug-resistant MTBC strains. Moreover, growth-inhibitory antimycobacterial activity of the combination of bedaquiline/pretomanid/linezolid was further enhanced by wollamide B1, and wollamide B1 did not compromise the antimycobacterial activity of the isoniazid/rifampicin/ethambutol combination. Collectively, these findings add new dimensions to the desirable characteristics of the wollamide pharmacophore as an antimycobacterial lead compound. IMPORTANCE Tuberculosis (TB) is an infectious disease that affects millions of people globally, with 1.6 million deaths annually. TB treatment requires combinations of multiple different antibiotics for many months, and toxic side effects can occur. Therefore, shorter, safer, more effective TB therapies are required, and these should ideally also be effective against drug-resistant strains of the bacteria that cause TB. This study shows that wollamide B1, a chemically optimized member of a new class of antibacterial compounds, inhibits the growth of drug-sensitive as well as multidrug-resistant Mycobacterium tuberculosis isolated from TB patients. In combination with TB antibiotics, wollamide B1 synergistically enhances the activity of several antibiotics, including complex drug combinations that are currently used for TB treatment. These new insights expand the catalogue of the desirable characteristics of wollamide B1 as an antimycobacterial lead compound that might inspire the development of improved TB treatments.
Collapse
Affiliation(s)
- Rachel F. Rollo
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giorgia Mori
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Doris Hillemann
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Antje Blumenthal
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
32
|
Dekhil N, Mardassi H. Genomic changes underpinning the emergence of a successful Mycobacterium tuberculosis Latin American and Mediterranean clonal complex. Front Microbiol 2023; 14:1159994. [PMID: 37425998 PMCID: PMC10325029 DOI: 10.3389/fmicb.2023.1159994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction The Latin American and Mediterranean sublineage (L4.3/LAM) is the most common generalist sublineage of Mycobacterium tuberculosis lineage 4 (L4), yet certain L4.3/LAM genotypes appear to be confined to particular geographic regions. This is typically the case of a L4.3/LAM clonal complex (CC), TUN4.3_CC1, which is the most preponderant in Tunisia (61.5% of L4.3/LAM). Methods Here, we used whole-genome sequencing data of 346 globally distributed L4 clinical strains, including 278 L4.3/LAM isolates, to reconstruct the evolutionary history of TUN4.3_CC1 and delineate critical genomic changes underpinning its success. Results and Discussion Phylogenomic coupled to phylogeographic analyses indicated that TUN4.3_CC1 has evolved locally, being confined mainly to North Africa. Maximum likelihood analyses using the site and branch-site models of the PAML package disclosed strong evidence of positive selection in the gene category "cell wall and cell processes" of TUN4.3_CC1. Collectively, the data indicate that TUN4.3_CC1 has inherited several mutations, which could have potentially contributed to its evolutionary success. Of particular interest are amino acid replacements at the esxK and eccC2 genes of the ESX/Type VII secretion system, which were found to be specific to TUN4.3_CC1, being common to almost all isolates. Because of its homoplastic nature, the esxK mutation could potentially have endowed TUN4.3_CC1 with a selective advantage. Moreover, we noticed the occurrence of additional, previously described homoplasic nonsense mutations in ponA1 and Rv0197. The mutation in the latter gene, a putative oxido-reductase, has previously been shown to be correlated with enhanced transmissibility in vivo. In sum, our findings unveiled several features underpinning the success of a locally evolved L4.3/LAM clonal complex, lending further support to the critical role of genes encoded by the ESX/type VII secretion system.
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Pérez-Llanos FJ, Dreyer V, Barilar I, Utpatel C, Kohl TA, Murcia MI, Homolka S, Merker M, Niemann S. Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region. Microbiol Spectr 2023; 11:e0501322. [PMID: 37222610 PMCID: PMC10269451 DOI: 10.1128/spectrum.05013-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.
Collapse
Affiliation(s)
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Martha Isabel Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| |
Collapse
|
35
|
Tao B, Li Z, Wang Y, Wu J, Shi X, Shi J, Liu Q, Wang J. Environment pollutants exposure affects the endogenous activation of within-host Mycobacterium tuberculosis. ENVIRONMENTAL RESEARCH 2023; 227:115695. [PMID: 36958381 DOI: 10.1016/j.envres.2023.115695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 05/08/2023]
Abstract
OBJECTIVE Epidemiological studies have linked ambient pollutants with tuberculosis (TB) risk, but the association has not been fully understood. Here, for the first time, we applied whole-genome sequencing (WGS) to assess the reproductive state of Mycobacterium tuberculosis (MTB) by profiling the mutation rate of MTB (MTBMR) during within-host endogenous reactivated progression, intending to dissect the actual effects of ambient pollutants on the endogenous reactivation. METHODS We conducted a retrospective cohort study on bacteriologically confirmed TB patients and followed them for relapse in Jiangsu and Sichuan Province, China. Endogenous and exogenous activation were distinguished by WGS of the pathogen. The average concentration of air pollution was estimated by considering a lag of 0-1 to 0-12 months. We applied a generalized additive model with a Poisson function to evaluate the relationships between ambient pollutants exposure and MTBMR. RESULTS In the single-pollutant adjusted models, the maximum effect for PM10 (MTBMR increase: 81.87%, 95% CI: 38.38, 139.03) and PM2.5 (MTBMR increase: 73.91%, 95% CI: 22.17, 147.55) was observed at a lag of 0-12 months for every 10 μg/m³ increase. For SO2, the maximum effect was observed at lag 0-8 months, with MTBMR increasing by 128.06% (95% CI: 45.92, 256.44); and for NO2, the maximum effect was observed at lag 0-9 months, with MTBMR increasing by 124.02% (95% CI: 34.5, 273.14). In contrast, the O3 concentration was inversely associated with MTBMR, and the maximum reduction of MTBMR was 6.18% (95% CI: -9.24, -3.02) at a lag of 0-9 months. Similar results were observed for multi-pollutant models. CONCLUSIONS Increased exposure to ambient pollutants (PM10, PM2.5, SO2, and NO2) contributed to a faster MTBMR, indicating that MTB exhibits increased reproductive activity, thus accelerating within-host endogenous reactivation. O3 exposure could decrease the MTBMR, suggesting that MTB exerts low reproductive activity by inhibiting within-host endogenous activation.
Collapse
Affiliation(s)
- Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Epidemiology, The Third People's Hospital of Changzhou, Changzhou, China; Department of Epidemiology, Gusu School, Nanjing Medical University, Nanjing, China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuting Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinling Shi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jinyan Shi
- Department of Clinical Laboratory, The Fourth People's Hospital of Lianyungang, Lianyungang, China
| | - Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China.
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Epidemiology, The Third People's Hospital of Changzhou, Changzhou, China; Department of Epidemiology, Gusu School, Nanjing Medical University, Nanjing, China.
| |
Collapse
|
36
|
Kim NY, Kim DY, Chu J, Jung SH. pncA Large Deletion is the Characteristic of Pyrazinamide-Resistant Mycobacterium tuberculosis belonging to the East Asian Lineage. Infect Chemother 2023; 55:247-256. [PMID: 37407242 DOI: 10.3947/ic.2023.0037] [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: 04/05/2023] [Accepted: 05/10/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Pyrazinamide (PZA) is often used as an add-on agent in the treatment of multidrug-resistant tuberculosis, regardless of phenotypic drug susceptibility testing (pDST) results. However, evaluating the effectiveness of PZA is challenging because of its low pH activity, which can result in unreliable pDST results. This study aimed to investigate the genomic characteristics associated with PZA resistance that can be used to develop genotypic DST. MATERIALS AND METHODS A publicly available whole genome sequencing (WGS) dataset of 10,725 Mycobacterium tuberculosis complex genomes (3,326 phenotypically PZA-resistant and 7,399 phenotypically PZA-susceptible isolates) were analyzed. RESULTS In total, 2,934 pncA non-silent mutations were identified in 2,880 isolates (26.9%). Detected mutations were found throughout the entire coding region of pncA in a scattered pattern, of which the most frequent mutation was p.Q10P (n = 278), followed by p.H57D (n = 167) and c.-11A>G (n = 122). The sensitivity and specificity of the group 1 or 2 mutations reported by the World Health Organization (WHO) mutational catalogue were 73.0% and 98.9%, respectively. We further identified 18 novel pncA mutations that were significantly associated with phenotypically PZA-resistant. In addition to these mutations, we identified 102 large deletions in the pncA gene, and all but two isolates were phenotypically resistant to PZA isolates. Notably, pncA deletions were mutually exclusive to pncA mutations, and more than half of the isolates with pncA large deletions belonged to the East Asian lineage (67.6%). The sensitivity, specificity, positive predictive value, and negative predictive value of the pooled variants (group 1 or 2 mutations, novel resistance-associated mutations, and large deletions of the pncA gene) were 79.0%, 98.9%, 97.0%, and 91.3%, respectively. The area under the curve (AUC) value for the pooled variants was significantly higher than the AUC value for the group 1 or 2 mutations (P <0.001), indicating that the pooled variants have a better discriminative ability for predicting PZA resistance. CONCLUSION Using WGS, we found that the pncA mutations are scattered without specific mutational hotspots, and large deletions associated with PZA resistance are more common in the East Asian lineage of M. tuberculosis isolates. Our data also demonstrated the reliability of group 1 or 2 mutations presented in the WHO mutation catalogue and the need for further investigation on group 3 mutations, contributing to the evaluation of the current knowledge base on mutations associated with the PZA-resistant M. tuberculosis complex.
Collapse
Affiliation(s)
- Na Yung Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Do Young Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyon Chu
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Biochemistry, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| |
Collapse
|
37
|
Ghazvini K, Khoshbakht R, Tadayon K, Mosavari N, BahramiTaghanaki HR, Mohammadi GR, Rashti Baf M, Nourian K, Samiei A, Ghavidel M. Genotyping of Mycobacterium tuberculosis complex isolated from humans and animals in northeastern Iran. Sci Rep 2023; 13:6746. [PMID: 37185604 PMCID: PMC10127167 DOI: 10.1038/s41598-023-33740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to genotype Mycobacterium tuberculosis complex isolated from humans and cattle in northern Iran. Over the course of one year, a total of 120 human and 21 cattle isolates were tested using region of difference (RD)-based polymerase chain reaction (PCR) and mycobacterial interspersed repetitive unites-variable number tandem repeats (MIRU-VNTR). In M. tuberculosis, out of 120 isolates investigated, the most common genotype detected was NEW-1 (53.3%), followed by CAS/ Delhi (24.1%), Haarlem (5%), Beijing (4.16%), Uganda I (4.16%), S (3.3%), Ural (0.83%), TUR (0.83%), Uganda II (0.83%), Lam (0.83%) and Cameroon (0.83%). The HGDI rate was 0.9981 and the clustering rate was 10.83. Of the isolates, QUB26 had the highest allele diversity (h: 0.76), while the loci Mtub29 and MIRU24 had the lowest (h: 0). In M. Bovis, out of 123 collected tissue samples, 21 (17%) grew on culture media. The HGDI rate was 0.71 and clustering rate was 85.7%. The locus ETRC had the highest allele diversity (h: 0.45). The findings of this study suggest that there is high genetic diversity among M. tuberculosis isolates in Khorasan Razavi Province, which is consistent with similar results from other studies in other provinces in Iran and neighboring countries. This indicates that the prevalent genotypes in this study are spreading in the Middle East region. Furthermore, considering that M. Bovis isolates were identified in two clusters, it seems that all of them have a common origin and are circulating among the livestock farms in the province.
Collapse
Affiliation(s)
- Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Khoshbakht
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Rashti Baf
- Deputy of Veterinary Administration of Khorasan Razavi Province, Mashhad, Iran
| | - Kimiya Nourian
- Department of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Samiei
- Tuberculosis and Leprosy Coordinator at Health Chancellor, Health Center of Khorasan State, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdis Ghavidel
- Shahid Hasheminejad Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
38
|
Laamarti M, El Fathi Lalaoui Y, Elfermi R, Daoud R, El Allali A. Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa. Sci Data 2023; 10:212. [PMID: 37059737 PMCID: PMC10102689 DOI: 10.1038/s41597-023-02112-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this bacterium causes disease, how the immune system responds to it, how it has evolved over time, and how it is distributed geographically. However, despite extensive research efforts, the evolution and transmission of MTB in Africa remain poorly understood. In this study, we used 17,641 strains from 26 countries to create the first curated African Mycobacterium tuberculosis (MTB) classification and resistance dataset, containing 13,753 strains. We identified 157 mutations in 12 genes associated with resistance and additional new mutations potentially associated with resistance. The resistance profile was used to classify strains. We also performed a phylogenetic classification of each isolate and prepared the data in a format that can be used for phylogenetic and comparative analysis of tuberculosis worldwide. These genomic data will extend current information for comparative genomic studies to understand the mechanisms and evolution of MTB drug resistance.
Collapse
Affiliation(s)
- Meriem Laamarti
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | | | - Rachid Elfermi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| |
Collapse
|
39
|
Bakuła Z, Marczak M, Bluszcz A, Proboszcz M, Kościuch J, Krenke R, Stakėnas P, Mokrousov I, Jagielski T. Phylogenetic relationships of Mycobacterium tuberculosis isolates in Poland: The emergence of Beijing genotype among multidrug-resistant cases. Front Cell Infect Microbiol 2023; 13:1161905. [PMID: 37009494 PMCID: PMC10061152 DOI: 10.3389/fcimb.2023.1161905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
IntroductionThe epidemiological situation of tuberculosis (TB) in Poland urges for its continuous and scrupulous monitoring. The objective of this study was to explore the genetic diversity of multidrug-resistant (MDR) and drug-susceptible (DS) Mycobacterium tuberculosis isolates from Poland with a combination of spoligotyping and high-resolution mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis. The results were placed in the Northern and Eastern Europe context.MethodsThe study included 89 (39 MDR and 50 DS) M. tuberculosis isolates collected from as many patients between 2018 and 2021 in Poland. The analysis was done using spoligotyping, and MIRU-VNTR typing at 24 standard loci. The data were compared to those available on Poland and neighbors and global M. tuberculosis datasets.ResultsThe main identified families were Beijing (28.1%) and Haarlem (16.8%) while 34.8% of isolates were in the heterogeneous L4-unclassified group. Although the Beijing family was the most prevalent (61.5%) among MDR-TB cases, it accounted for only 2% of DS isolates. Among foreign-born patients, a higher ratio of MDR isolates were observed when compared with those who Poland-born (64.3% vs. 40%). Furthermore, all patients from the Former Soviet Union (FSU) countries were infected with MDR-TB.DiscussionWhereas DS M. tuberculosis population in Poland is dominated by L4 isolates, MDR isolates are mostly of the Beijing genotype. The rise in the prevalence of the Beijing isolates in Poland, coupled with high proportion of the Beijing genotype among foreign-born TB patients may reflect an ongoing transmission of this family, imported to Poland mainly from FSU countries.
Collapse
Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Mateusz Marczak
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Agata Bluszcz
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Justyna Kościuch
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Petras Stakėnas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland
- *Correspondence: Tomasz Jagielski, ; Igor Mokrousov,
| |
Collapse
|
40
|
Perchlozone Resistance in Clinical Isolates of Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:antibiotics12030590. [PMID: 36978456 PMCID: PMC10044601 DOI: 10.3390/antibiotics12030590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The emergence of drug-resistant tuberculosis forced the development of new drugs and the screening of more effective or less toxic analogues. Mycolic acid biosynthesis is targeted by several antituberculosis drugs, isoniazid being one of the most important in tuberculosis therapy. Recently, perchlozone, acting on another step in the FAS-II cycle, was officially approved for tuberculosis treatment in the Russian Federation and was included in the Russian national clinical guidelines. Using the serial dilution method on 7H10 agar plates for perchlozone and a Sensititre MYCOTB microdilution plate, we analyzed the phenotypic properties of primary clinical isolates of M. tuberculosis and analyzed the molecular determinants of resistance to isoniazid, ethionamide, and perchlozone. We found a wide variation in the MIC of perchlozone from 2 to 64 mg/L, correlating with the overall resistance profile: the MIC was higher for MDR and pre-XDR isolates. The cross-resistance between ethionamide and perchlozone was driven by mutations in the ethA gene encoding monooxygenase responsible for the activation of both drugs. The presumably susceptible to perchlozone and wild-type strains had MICs ranging from 2 to 4 mg/L, and the breakpoint was estimated to be 4 or 8 mg/L. In conclusion, susceptibility to perchlozone is retained for a part of the MDR strains, as is susceptibility to ethionamide, providing the possibility of therapy for such cases based on phenotypic or molecular analysis.
Collapse
|
41
|
Jiang Q, Liu HC, Liu QY, Phelan JE, Tao FX, Zhao XQ, Wang J, Glynn JR, Takiff HE, Clark TG, Wan KL, Gao Q. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiol Spectr 2023; 11:e0399122. [PMID: 36912683 PMCID: PMC10101056 DOI: 10.1128/spectrum.03991-22] [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: 10/06/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
On the Tibetan Plateau, most tuberculosis is caused by indigenous Mycobacterium tuberculosis strains with a monophyletic structure and high-level drug resistance. This study investigated the emergence, evolution, and transmission dynamics of multidrug-resistant tuberculosis (MDR-TB) in Tibet. The whole-genome sequences of 576 clinical strains from Tibet were analyzed with the TB-profiler tool to identify drug-resistance mutations. The evolution of the drug resistance was then inferred based on maximum-likelihood phylogeny and dated trees that traced the serial acquisition of mutations conferring resistance to different drugs. Among the 576 clinical M. tuberculosis strains, 346 (60.1%) carried at least 1 resistance-conferring mutation and 231 (40.1%) were MDR-TB. Using a pairwise distance of 50 single nucleotide polymorphisms (SNPs), most strains (89.9%, 518/576) were phylogenetically separated into 50 long-term transmission clusters. Eleven large drug-resistant clusters contained 76.1% (176/231) of the local multidrug-resistant strains. A total of 85.2% of the isoniazid-resistant strains were highly transmitted with an average of 6.6 cases per cluster, of which most shared the mutation KatG Ser315Thr. A lower proportion (71.6%) of multidrug-resistant strains were transmitted, with an average cluster size of 2.9 cases. The isoniazid-resistant clusters appear to have undergone substantial bacterial population growth in the 1970s to 1990s and then subsequently accumulated multiple rifampicin-resistance mutations and caused the current local MDR-TB burden. These findings highlight the importance of detecting and curing isoniazid-resistant strains to prevent the emergence of endemic MDR-TB. IMPORTANCE Emerging isoniazid resistance in the 1970s allowed M. tuberculosis strains to spread and form into large multidrug-resistant tuberculosis clusters in the isolated plateau of Tibet, China. The epidemic was driven by the high risk of transmission as well as the potential of acquiring further drug resistance from isoniazid-resistant strains. Eleven large drug-resistant clusters consisted of the majority of local multidrug-resistant cases. Among the clusters, isoniazid resistance overwhelmingly evolved before all the other resistance types. A large bacterial population growth of isoniazid-resistant clusters occurred between 1970s and 1990s, which subsequently accumulated rifampicin-resistance-conferring mutations in parallel and accounted for the local multidrug-resistant tuberculosis burden. The results of our study indicate that it may be possible to restrict MDR-TB evolution and dissemination by prioritizing screening for isoniazid (INH)-resistant TB strains before they become MDR-TB and by adopting measures that can limit their transmission.
Collapse
Affiliation(s)
- Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Hai-Can Liu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing-Yun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jody E. Phelan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Feng-Xi Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Xiu-Qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jian Wang
- Tibet Center for Disease Control and Prevention, Lhasa, Tibet Autonomous Region, China
| | - Judith R. Glynn
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Howard E. Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kang-Lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Gao
- National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong, China
| |
Collapse
|
42
|
Spatial patterns of tuberculosis in Russia in the context of social determinants. Spat Spatiotemporal Epidemiol 2023. [DOI: 10.1016/j.sste.2023.100580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
43
|
Genetic Diversity and Primary Drug Resistance of Mycobacterium tuberculosis Beijing Genotype Strains in Northwestern Russia. Microorganisms 2023; 11:microorganisms11020255. [PMID: 36838219 PMCID: PMC9966048 DOI: 10.3390/microorganisms11020255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
The Beijing genotype is the main family of Mycobacterium tuberculosis in Russia. We analyzed its diversity and drug resistance in provinces across Northwestern Russia to identify the epidemiologically relevant Beijing strains. The study collection included 497 isolates from newly-diagnosed tuberculosis (TB) patients. Bacterial isolates were subjected to drug-susceptibility testing and genotyping. The Beijing genotype was detected in 57.5% (286/497); 50% of the Beijing strains were multidrug-resistant (MDR). Central Asian/Russian and B0/W148 groups included 176 and 77 isolates, respectively. MDR was more frequent among B0/W148 strains compared to Central Asian/Russian strains (85.7% vs. 40.3%, p < 0.0001). Typing of 24 minisatellite loci of Beijing strains revealed 82 profiles; 230 isolates were in 23 clusters. The largest Central Asian/Russian types were 94-32 (n = 75), 1065-32 (n = 17), and 95-32 (n = 12). B0/W148 types were 100-32 (n = 59) and 4737-32 (n = 5). MDR was more frequent in types 1065-32 (88.2%), 100-32 (83.1%), and 4737-32 (100%). In contrast, type 9391-32 (n = 9) included only drug-susceptible strains. To conclude, M. tuberculosis Beijing genotype is dominant in Northwestern Russia, and an active transmission of overwhelmingly MDR B0/W148 types explains the reported increase of MDR-TB. The presence of MDR-associated minor variants (type 1071-32/ancient Beijing and Central Asia Outbreak strain) in some of the studied provinces also requires attention.
Collapse
|
44
|
Hurtado-Páez U, Álvarez Zuluaga N, Arango Isaza RE, Contreras-Moreira B, Rouzaud F, Robledo J. Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia. Front Microbiol 2023; 13:1076797. [PMID: 36687645 PMCID: PMC9846648 DOI: 10.3389/fmicb.2022.1076797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.
Collapse
Affiliation(s)
- Uriel Hurtado-Páez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,*Correspondence: Uriel Hurtado-Páez,
| | | | - Rafael Eduardo Arango Isaza
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Facultad de Ciencias, Universidad Nacional de Colombia (UNAL), Medellín, Colombia
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei–Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain,Fundación ARAID, Zaragoza, Spain
| | | | - Jaime Robledo
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia
| |
Collapse
|
45
|
Skhairia MA, Dekhil N, Mardassi H. Evolutionary history and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage, Tunisia. Tuberculosis (Edinb) 2023; 138:102297. [PMID: 36584485 DOI: 10.1016/j.tube.2022.102297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND To infer the origin and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in a Mediterranean country, Tunisia, where it predominates. METHODS We combined Bayesian (STRUCTURE) and maximum likelihood (MIGRAINE) estimation approaches based on a global 24-loci mycobacterial interspersed repetitive units-variable numbers of tandem repeats (MIRU-VNTR24) genotyping dataset consisting of 1573 L4.3/LAM clinical strains from four continents, including 252 isolates originating from Tunisia. RESULTS Phylogenetic analyses coupled with Bayesian estimations suggested that the most predominant L4.3/LAM subpopulation in Tunisia (65.07%), which is dominated by a single clonal complex, TUN4.3_CC1 (94.51%), has evolved from an ancestral pool that is restricted to Europe and Africa, contrasting with the remaining L4.3/LAM subpopulations whose ancestry was traced all over the word. Maximum likelihood analysis revealed that TUN4.3_CC1 has been undergoing a demographic expansion since 131 years ago (CI95%: 90.7-205), thus explaining its preponderance relative to the second most predominant CC, TUN4.3_CC2, whose population was found under contraction. CONCLUSIONS The preponderance of L4.3/LAM in Tunisia stems from a 130-year expansion process of a locally evolved clone.
Collapse
Affiliation(s)
- Mohamed Amine Skhairia
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
| |
Collapse
|
46
|
Berube BJ, Larsen SE, McNeil MB, Reese VA, Pecor T, Kaur S, Parish T, Baldwin SL, Coler RN. Characterizing in vivo loss of virulence of an HN878 Mycobacterium tuberculosis isolate from a genetic duplication event. Tuberculosis (Edinb) 2022; 137:102272. [PMID: 36375278 PMCID: PMC10019580 DOI: 10.1016/j.tube.2022.102272] [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: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022]
Abstract
The increase of global cases of drug resistant (DR) Mycobacterium tuberculosis (M.tb) is a serious problem for the tuberculosis research community and the goals to END TB by 2030. Due to the need for advancing and screening next generation therapeutics and vaccines, we aimed to design preclinical DR models of Beijing lineage M.tb HN878 strain in different mouse backgrounds. We found escalating sensitivities of morbidity due to low dose aerosol challenge (50-100 bacilli) in CB6F1, C57BL/6 and SWR mice, respectively. We also observed that pulmonary bacterial burden at morbidity endpoints correlated inversely with survival over time between mouse strains. Interestingly, with in vitro passaging and in the process of selecting individual DR mutant colonies, we observed a significant decrease in in vivo HN878 strain virulence, which correlated with the acquisition of a large genetic duplication. We confirmed that low passage infection stocks with no or low prevalence of the duplication, including stocks directly acquired from the BEI resources biorepository, retained virulence, measured by morbidity over time. These data help confirm previous reports and emphasize the importance of monitoring virulence and stock fidelity.
Collapse
Affiliation(s)
- Bryan J Berube
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Sasha E Larsen
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Valerie A Reese
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tiffany Pecor
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Suhavi Kaur
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tanya Parish
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Susan L Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Rhea N Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
| |
Collapse
|
47
|
Rajwani R, Galata C, Lee AWT, So PK, Leung KSS, Tam KKG, Shehzad S, Ng TTL, Zhu L, Lao HY, Chan CTM, Leung JSL, Lee LK, Wong KC, Yam WC, Siu GKH. A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis. Virulence 2022; 13:1088-1100. [PMID: 35791449 PMCID: PMC9262360 DOI: 10.1080/21505594.2022.2087304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical manifestations of tuberculosis range from asymptomatic infection to a life-threatening disease such as tuberculous meningitis (TBM). Recent studies showed that the spectrum of disease severity could be related to genetic diversity among clinical strains of Mycobacterium tuberculosis (Mtb). Certain strains are reported to preferentially invade the central nervous system, thus earning the label “hypervirulent strains”.However, specific genetic mutations that accounted for enhanced mycobacterial virulence are still unknown. We previously identified a set of 17 mutations in a hypervirulent Mtb strain that was from TBM patient and exhibited significantly better intracellular survivability. These mutations were also commonly shared by a cluster of globally circulating hyper-virulent strains. Here, we aimed to validate the impact of these hypervirulent-specific mutations on the dysregulation of gene networks associated with virulence in Mtb via multi-omic analysis. We surveyed transcriptomic and proteomic differences between the hyper-virulent and low-virulent strains using RNA-sequencing and label-free quantitative LC-MS/MS approach, respectively. We identified 25 genes consistently differentially expressed between the strains at both transcript and protein level, regardless the strains were growing in a nutrient-rich or a physiologically relevant multi-stress condition (acidic pH, limited nutrients, nitrosative stress, and hypoxia). Based on integrated genomic-transcriptomic and proteomic comparisons, the hypervirulent-specific mutations in FadE5 (g. 295,746 C >T), Rv0178 (p. asp150glu), higB (p. asp30glu), and pip (IS6110-insertion) were linked to deregulated expression of the respective genes and their functionally downstream regulons. The result validated the connections between mutations, gene expression, and mycobacterial pathogenicity, and identified new possible virulence-associated pathways in Mtb.
Collapse
Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chala Galata
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Annie Wing Tung Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kenneth Siu Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kingsley King Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Timothy Ting Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Li Zhu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kin Chung Wong
- Department of Clinical Pathology, United Christian Hospital, Hong Kong Special Administrative Region, China
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| |
Collapse
|
48
|
Ness TE, DiNardo A, Farhat MR. High Throughput Sequencing for Clinical Tuberculosis: An Overview. Pathogens 2022; 11:pathogens11111343. [PMID: 36422596 PMCID: PMC9695813 DOI: 10.3390/pathogens11111343] [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: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
High throughput sequencing (HTS) can identify the presence of Mycobacterium tuberculosis DNA in a clinical sample while also providing information on drug susceptibility. Multiple studies have provided a context for exploring the clinical application of HTS for TB diagnosis. The workflow challenges, strengths and limitations of the various sequencing platforms, and tools used for analysis are presented to provide a framework for further innovations in the field.
Collapse
Affiliation(s)
- Tara E. Ness
- Division of Pediatric Infectious Diseases, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX 77030, USA
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
- Correspondence:
| | - Andrew DiNardo
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
| | - Maha R. Farhat
- Harvard Medical School Biomedical Informatics and Pulmonary and Critical Care Massachusetts General Hospital, Boston, MA 02115, USA
| |
Collapse
|
49
|
Whole-Genome Sequencing for Resistance Prediction and Transmission Analysis of Mycobacterium tuberculosis Complex Strains from Namibia. Microbiol Spectr 2022; 10:e0158622. [PMID: 36165641 PMCID: PMC9603870 DOI: 10.1128/spectrum.01586-22] [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] [Indexed: 12/31/2022] Open
Abstract
Namibia is among 30 countries with a high burden of tuberculosis (TB), with an estimated incidence of 460 per 100,000 population and around 800 new multidrug-resistant (MDR) TB cases per year. Still, data on the transmission and evolution of drug-resistant Mycobacterium tuberculosis complex (Mtbc) strains are not available. Whole-genome sequencing data of 136 rifampicin-resistant (RIFr) Mtbc strains obtained from 2016 to 2018 were used for phylogenetic classification, resistance prediction, and cluster analysis and linked with phenotypic drug susceptibility testing (pDST) data. Roughly 50% of the strains investigated were resistant to all first-line drugs. Furthermore, 13% of the MDR Mtbc strains were already pre-extensively drug resistant (pre-XDR). The cluster rates were high, at 74.6% among MDR and 85% among pre-XDR strains. A significant proportion of strains had borderline resistance-conferring mutations, e.g., inhA promoter mutations or rpoB L430P. Accordingly, 25% of the RIFr strains tested susceptible by pDST. Finally, we determined a potentially new bedaquiline resistance mutation (Rv0678 D88G) occurring in two independent clusters. High rates of resistance to first-line drugs in line with emerging pre-XDR and likely bedaquiline resistance linked with the ongoing recent transmission of MDR Mtbc clones underline the urgent need for the implementation of interventions that allow rapid diagnostics to break MDR TB transmission chains in the country. A borderline RIFr mutation in the dominant outbreak strain causing discrepancies between phenotypic and genotypic resistance testing results may require breakpoint adjustments but also may allow individualized regimens with high-dose treatment. IMPORTANCE The transmission of drug-resistant tuberculosis (TB) is a major problem for global TB control. Using genome sequencing, we showed that 13% of the multidrug-resistant (MDR) M. tuberculosis complex strains from Namibia are already pre-extensively drug resistant (pre-XDR), which is substantial in an African setting. Our data also indicate that the ongoing transmission of MDR and pre-XDR strains contributes significantly to the problem. In contrast to other settings with higher rates of drug resistance, we found a high proportion of strains having so-called borderline low-level resistance mutations, e.g., inhA promoter mutations or rpoB L430P. This led to the misclassification of 25% of the rifampicin-resistant strains as susceptible by phenotypic drug susceptibility testing. This observation potentially allows individualized regimens with high-dose treatment as a potential option for patients with few treatment options. We also found a potentially new bedaquiline resistance mutation in rv0678.
Collapse
|
50
|
Al-Mutairi NM, Ahmad S, Mokaddas E, Al-Hajoj S. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Kuwait and evaluation of REBA MTB-MDR assay for rapid detection of MDR-TB. PLoS One 2022; 17:e0276487. [PMID: 36264939 PMCID: PMC9584360 DOI: 10.1371/journal.pone.0276487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Early detection of Mycobacterium tuberculosis (Mtb) in clinical specimens, its susceptibility to anti-TB drugs and disruption of infection transmission to new hosts are essential components for global tuberculosis (TB) control efforts. This study investigated major Mtb genotypes circulating in Kuwait and evaluated the performance of REBA MTB-MDR (REBA) test in comparison to GenoType MTBDRplus (gMTBDR+) assay for rapid detection of resistance of Mtb to isoniazid and rifampicin (MDR-TB). M. tuberculosis isolates (n = 256) originating predominantly from expatriate patients during a 6-month period were tested by spoligotyping and a dendrogram was created by UPGMA using MIRU-VNTRplus software. Phenotypic drug susceptibility testing (DST) was performed by MGIT 960 system. Genotypic DST for isoniazid and rifampicin was done by REBA and gMTBDR+ assays. Spoligotyping assigned 188 (73.4%) isolates to specific spoligotype international type (SIT) while 68 isolates exhibited orphan patterns. All major M. tuberculosis lineages were detected and EAI, CAS and Beijing families were predominant. Phylogenetic tree showed 131 patterns with 105 isolates exhibiting a unique pattern while 151 isolates clustered in 26 patterns. Fifteen isolates were resistant to one/more drugs. REBA and gMTBDR+ detected isoniazid resistance in 11/12 and 10/12 and rifampicin resistance in 4/5 and 4/5 resistant isolates, respectively. The diversity of SIT patterns are highly suggestive of infection of most expatriate patients with unique Mtb strains, likely acquired in their native countries before their arrival in Kuwait. Both, REBA and gMTBDR+ assays performed similarly for detection of resistance of Mtb to isoniazid and rifampicin for rapid detection of MDR-TB.
Collapse
Affiliation(s)
- Noura M. Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail: ,
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Special Hospital and Research Center (KFSH & RC), Riyadh, Saudi Arabia
| |
Collapse
|