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Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu ZM, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D. Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania. Sci Rep 2024; 14:9287. [PMID: 38653771 DOI: 10.1038/s41598-024-60001-0] [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: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aimed to assess if bacterial genetics governs MTBC pathogenesis or if local co-adaptation translates into differential susceptibility of human macrophages to infection by different MTBC genotypes. We generated macrophages from cryopreserved blood mononuclear cells of Tanzanian tuberculosis patients, from which the infecting MTBC strains had previously been phylogenetically characterized. We infected these macrophages ex vivo with a phylogenetically similar MTBC strain ("matched infection") or with strains representative of other MTBC lineages ("mismatched infection"). We found that L1 infections resulted in a significantly lower bacterial burden and that the intra-cellular replication rate of L2 strains was significantly higher compared the other MTBC lineages, irrespective of the MTBC lineage originally infecting the patients. Moreover, L4-infected macrophages released significantly greater amounts of TNF-α, IL-6, IL-10, MIP-1β, and IL-1β compared to macrophages infected by all other strains. While our results revealed no measurable effect of local adaptation, they further highlight the strong impact of MTBC phylogenetic diversity on the variable outcome of the host-pathogen interaction in human tuberculosis.
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Affiliation(s)
- Hellen Hiza
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Michaela Zwyer
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jerry Hella
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Ainhoa Arbués
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mohamed Sasamalo
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Zhi Ming Xu
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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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: 2] [Impact Index Per Article: 2.0] [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.
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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
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Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia. PLoS One 2021; 16:e0253480. [PMID: 34252107 PMCID: PMC8274931 DOI: 10.1371/journal.pone.0253480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The present study investigated factors associated with M. tb lineage predominance and rate of strain clustering within urban and peri-urban settings in Ethiopia. Methods Pulmonary Tuberculosis (PTB) and Cervical tuberculous lymphadenitis (TBLN) patients who visited selected health facilities were recruited in the years of 2016 and 2017. A total of 258 M. tb isolates identified from 163 sputa and 95 fine-needle aspirates (FNA) were characterized by spoligotyping and compared with international M.tb spoligotyping patterns registered at the SITVIT2 databases. The molecular data were linked with clinical and demographic data of the patients for further statistical analysis. Results From a total of 258 M. tb isolates, 84 distinct spoligotype patterns that included 58 known Shared International Type (SIT) patterns and 26 new or orphan patterns were identified. The majority of strains belonged to two major M. tb lineages, L3 (35.7%) and L4 (61.6%). The observed high percentage of isolates with shared patterns (n = 200/258) suggested a substantial rate of overall clustering (77.5%). After adjusting for the effect of geographical variations, clustering rate was significantly lower among individuals co-infected with HIV and other concomitant chronic disease. Compared to L4, the adjusted odds ratio and 95% confidence interval (AOR; 95% CI) indicated that infections with L3 M. tb strains were more likely to be associated with TBLN [3.47 (1.45, 8.29)] and TB-HIV co-infection [2.84 (1.61, 5.55)]. Conclusion Despite the observed difference in strain diversity and geographical distribution of M. tb lineages, compared to earlier studies in Ethiopia, the overall rate of strain clustering suggests higher transmission and warrant more detailed investigations into the molecular epidemiology of TB and related factors.
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Spekker O, Schultz M, Paja L, Váradi OA, Molnár E, Pálfi G, Hunt DR. Tracking down the White Plague. Chapter two: The role of endocranial abnormal blood vessel impressions and periosteal appositions in the paleopathological diagnosis of tuberculous meningitis. PLoS One 2020; 15:e0238444. [PMID: 32870917 PMCID: PMC7462305 DOI: 10.1371/journal.pone.0238444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/17/2020] [Indexed: 12/17/2022] Open
Abstract
Although endocranial abnormal blood vessel impressions (ABVIs) and periosteal appositions (PAs) have been considered as paleopathological diagnostic criteria for tuberculous meningitis (TBM) based on findings of previous studies, they are not pathognomonic for tuberculosis (TB). Therefore, their utilization in the paleopathological practice can be questioned, especially in consideration that most of the previous studies were not performed on identified skeletal collections but on osteoarchaeological material and did not include statistical data analysis. To fill the aforementioned research gap, for the first time, a macroscopic investigation was conducted on identified pre-antibiotic era skeletons from the Terry Collection. A sample set of 234 individuals who died of TB (TB group) and 193 individuals who died of non-tuberculous causes (NTB group) were examined. The frequency of ABVIs and PAs, as well as other probable TB-related lesions was recorded. To determine the significance of difference (if any) in the frequencies of ABVIs and PAs between the two groups, χ2 testing of our data was performed. We found that ABVIs, PAs, and their co-occurrence with each other and with other probable TB-related lesions were more common in the TB group than in the NTB group. In addition, the χ2 comparative frequencies of ABVIs and PAs revealed a statistically significant difference between individuals who died of TB and individuals who died of NTB causes. Our findings strengthen those of previous studies that ABVIs and PAs are not specific to TBM but can be of tuberculous origin. Therefore, they do have a diagnostic value in the identification of TB in human osteoarchaeological material, especially when they simultaneously occur with other probable TB-related lesions. Their prudent utilization provides paleopathologists with a stronger basis for diagnosing TB and consequently, a more sensitive means of assessing TB frequency in past human populations.
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Affiliation(s)
- Olga Spekker
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
- * E-mail:
| | - Michael Schultz
- Institut für Anatomie und Embryologie, Zentrum Anatomie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - László Paja
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Orsolya A. Váradi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - David R. Hunt
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, District of Columbia, Washington, D.C., United States of America
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Sharma K, Verma R, Advani J, Chatterjee O, Solanki HS, Sharma A, Varma S, Modi M, Ray P, Mukherjee KK, Sharma M, Dhillion MS, Suar M, Chatterjee A, Pandey A, Prasad TSK, Gowda H. Whole Genome Sequencing of Mycobacterium tuberculosis Isolates From Extrapulmonary Sites. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:413-425. [PMID: 28692415 DOI: 10.1089/omi.2017.0070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide. Extrapulmonary tuberculosis (EPTB) constitutes around 15-20% of TB cases in immunocompetent individuals. Extrapulmonary sites that are affected by TB include bones, lymph nodes, meningitis, pleura, and genitourinary tract. Whole genome sequencing has emerged as a powerful tool to map genetic diversity among Mycobacterium tuberculosis (MTB) isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission. Several pulmonary isolates of MTB have been sequenced over the years. However, availability of whole genome sequences of MTB isolates from extrapulmonary sites is limited. Some studies suggest that genetic variations in MTB might contribute to disease presentation in extrapulmonary sites. This can be addressed if whole genome sequence data from large number of extrapulmonary isolates becomes available. In this study, we have performed whole genome sequencing of five MTB clinical isolates derived from EPTB sites using next-generation sequencing platform. We identified 1434 nonsynonymous single nucleotide variations (SNVs), 143 insertions and 105 deletions. This includes 279 SNVs that were not reported before in publicly available datasets. We found several mutations that are known to confer resistance to drugs. All the five isolates belonged to East-African-Indian lineage (lineage 3). We identified 9 putative prophage DNA integrations and 14 predicted clustered regularly interspaced short palindromic repeats (CRISPR) in MTB genome. Our analysis indicates that more work is needed to map the genetic diversity of MTB. Whole genome sequencing in conjunction with comprehensive drug susceptibility testing can reveal clinically relevant mutations associated with drug resistance.
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Affiliation(s)
- Kusum Sharma
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | - Renu Verma
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Jayshree Advani
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Manipal University , Manipal, India
| | - Oishi Chatterjee
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,5 School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Hitendra S Solanki
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Aman Sharma
- 6 Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Subhash Varma
- 6 Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Manish Modi
- 7 Department of Neurology, PGIMER, Chandigarh, India
| | - Pallab Ray
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | | | - Megha Sharma
- 1 Department of Medical Microbiology, PGIMER , Chandigarh, India
| | | | - Mrutyunjay Suar
- 3 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Aditi Chatterjee
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India
| | - Akhilesh Pandey
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,11 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,13 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland.,14 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Thottethodi Subrahmanya Keshava Prasad
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India .,15 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
| | - Harsha Gowda
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India .,10 YU-IOB Center for Systems Biology and Molecular Medicine , Mangalore, India
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