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Tuberculosis attributed to transmission within healthcare facilities, Botswana—The Kopanyo Study. Infect Control Hosp Epidemiol 2022; 43:1603-1609. [DOI: 10.1017/ice.2021.517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Objective:
Healthcare facilities are a well-known high-risk environment for transmission of M. tuberculosis, the etiologic agent of tuberculosis (TB) disease. However, the link between M. tuberculosis transmission in healthcare facilities and its role in the general TB epidemic is unknown. We estimated the proportion of overall TB transmission in the general population attributable to healthcare facilities.
Methods:
We combined data from a prospective, population-based molecular epidemiologic study with a universal electronic medical record (EMR) covering all healthcare facilities in Botswana to identify biologically plausible transmission events occurring at the healthcare facility. Patients with M. tuberculosis isolates of the same genotype visiting the same facility concurrently were considered an overlapping event. We then used TB diagnosis and treatment data to categorize overlapping events into biologically plausible definitions. We calculated the proportion of overall TB cases in the cohort that could be attributable to healthcare facilities.
Results:
In total, 1,881 participants had TB genotypic and EMR data suitable for analysis, resulting in 46,853 clinical encounters at 338 healthcare facilities. We identified 326 unique overlapping events involving 370 individual patients; 91 (5%) had biologic plausibility for transmission occurring at a healthcare facility. A sensitivity analysis estimated that 3%–8% of transmission may be attributable to healthcare facilities.
Conclusions:
Although effective interventions are critical in reducing individual risk for healthcare workers and patients at healthcare facilities, our findings suggest that development of targeted interventions aimed at community transmission may have a larger impact in reducing TB.
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The potential risk of international spread of Mycobacterium bovis associated with movement of alpacas. J Vet Res 2022; 66:53-59. [PMID: 35434415 PMCID: PMC8959691 DOI: 10.2478/jvetres-2022-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 02/02/2023] Open
Abstract
Introduction The study highlights the transboundary nature of tuberculosis (TB) in alpacas and the failure of current ante-mortem testing protocols (the tuberculin skin and Enferplex Camelid TB tests) to identify TB-free alpaca herds and individuals for export. Our research and the available literature indicate that the alpaca (Vicugna pacos) is extremely susceptible to Mycobacterium bovis infection, and that testing periodicity fails to take into account that animals do not manifest disease symptoms for a long time. The skin test failed to identify Mycobacterium bovis infection in two alpacas prior to their movement from the UK to Poland. The animals were purchased by a breeding centre in Poland, and were then shown at an international animal exhibition. The last owner of the alpacas before their deaths from TB bought the infected animals unwittingly in order to run rehabilitation activities with disabled children on his farm. Material and Methods Thoracic lymph node, lung and liver tissue samples obtained at necropsy were examined histopathologically after Ziehl–Neelsen staining. Tissue samples were homogenised and mycobacteria present there were cultured on Stonebrink’s medium during a 6-week incubation. A commercial test using polymorphism of the chromosomal direct repeat region provided species identification and additional identification was by spacer oligonucleotide typing and mycobacteria interspersed repetitive unit–variable number tandem repeat analysis with a gel electrophoresis protocol. Results The microbiological examination confirmed multiorgan TB caused by the SB0666 spoligotype of Mycobacterium bovis. Conclusion Due to the suboptimal performance of current diagnostic tests for TB in alpacas, there is a risk that infected animals may be moved unwittingly. A risk of TB spread associated with the international movement of alpacas is implied by this study.
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Comín J, Otal I, Samper S. In-depth Analysis of IS 6110 Genomic Variability in the Mycobacterium tuberculosis Complex. Front Microbiol 2022; 13:767912. [PMID: 35283840 PMCID: PMC8912993 DOI: 10.3389/fmicb.2022.767912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The insertion sequence (IS) 6110 is a repetitive mobile element specific for the Mycobacterium tuberculosis complex (MTBC) used for years to diagnose and genotype this pathogen. It contains the overlapping reading frames orfA and orfB that encode a transposase. Its genetic variability is difficult to study because multiple copies are present in the genome. IS6110 is randomly located, nevertheless some preferential locations have been reported, which could be related to the behaviour of the strains. The aim of this work was to determine the intra- and inter-strain genetic conservation of this element in the MTBC. For this purpose, we analysed 158 sequences of IS6110 copies from 55 strains. Eighty-four copies were from 17 strains for which we knew all the locations in their genome. In addition, we studied 74 IS6110 copies in 38 different MTBC strains in which the location was characteristic of different families including Haarlem, LAM, S, and L6 strains. We observed mutation in 13.3% of the copies studied and we found 10 IS6110 variants in 21 copies belonging to 16 strains. The high copy number strains showed 6.2% of their IS6110 copies mutated, in contrast with the 31.1% in the low-copy-number strains. The apparently more ancient copy localised in the DR region was that with more variant copies, probably because this was the most studied location. Notably, all Haarlem and X family strains studied have an IS6110 in Rv0403c, suggesting a common origin for both families. Nevertheless, we detected a variant specific for the X family that would have occurred in this location after the phylogenetic separation. This variant does not prevent transposition although it may occur at a lower frequency, as X strains remain with low copy number (LCN) of IS6110.
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Affiliation(s)
- Jessica Comín
- Unidad de Investigación Traslacional, Hospital Universitario Miguel Servet, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación IIS Aragón, Zaragoza, Spain
| | - Isabel Otal
- Fundación IIS Aragón, Zaragoza, Spain.,Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Sofía Samper
- Unidad de Investigación Traslacional, Hospital Universitario Miguel Servet, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación IIS Aragón, Zaragoza, Spain.,CIBER de Enfermedades Respiratorias, Madrid, Spain
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Maghradze N, Jugheli L, Borrell S, Tukvadze N, Kempker RR, Blumberg HM, Gagneux S. Developing customized stepwise MIRU-VNTR typing for tuberculosis surveillance in Georgia. PLoS One 2022; 17:e0264472. [PMID: 35231041 PMCID: PMC8887741 DOI: 10.1371/journal.pone.0264472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction
Mycobacterial Interspersed Repetitive Units–Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia.
Methods
We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method.
Results
For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each.
Conclusion
Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings.
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Affiliation(s)
- Nino Maghradze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Levan Jugheli
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nestani Tukvadze
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Henry M. Blumberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States of America
- Departments of Epidemiology and Global Health, Rollins School of Public Health of Emory University, Atlanta, GA, United States of America
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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Chen J, Chen L, Zhou M, Wu G, Yi F, Jiang C, Duan Q, Zhou M. Transmission of multidrug-resistant tuberculosis within family households by DTM-PCR and MIRU-VNTR genotyping. BMC Infect Dis 2022; 22:192. [PMID: 35219320 PMCID: PMC8881899 DOI: 10.1186/s12879-022-07188-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Drug-resistant tuberculosis (TB) continues to be a public health threat. There are few studies on transmission and genotyping of MDR-TB family households in China. This study aimed to investigate transmission of multidrug-resistant tuberculosis (MDR-TB) within family households by deletion-targeted multiplex polymerase chain reaction (DTM-PCR), mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) genotyping.
Methods Among 993 MDR-TB patients registered from Wuhan Institute for Tuberculosis Control, drug resistance and the time interval between the index patients and secondary patients were analyzed in 49 MDR-TB patients from 23 families, in which 22 MDR-TB strains from 11 families who had matched strains were genotyped by DTM-PCR and standard 24-loci MIRU-VNTR genotyping method. Results The time interval between the index patients and the secondary patients ranged from half a month to 110 months. Thirteen secondary patients developed active MDR-TB within two years and accounted for 50% (13/26) of all secondary patients. Among eleven pairs of MDR-TB families, six pairs had identical genotypes, the cluster rate was 54.5% (12/22); three pairs had a single MIRU-VNTR locus variation. If a single MIRU-VNTR locus variation was tolerated in the cluster definition, the cluster rate raised to 81.8% (18/22). Conclusions The family households of MDR-TB patients are at risk for infection of MDR-TB. To reduce transmission, MDR-TB patients should be diagnosed earlier and promptly treated in an effective manner, meanwhile, the close family contacts should be screened for TB infection.
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Acosta F, Martínez-Lirola M, Sola-Campoy PJ, Sicilia J, Guerra-Galán T, Maus SR, Muñoz P, Pérez-Lago L, García de Viedma D. Insights into the Complexity of a Dormant Mycobacterium tuberculosis Cluster Once Transmission Is Resumed. Microbiol Spectr 2022; 10:e0138121. [PMID: 35044196 PMCID: PMC8768656 DOI: 10.1128/spectrum.01381-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022] Open
Abstract
Genotyping tools help identify the complexity in Mycobacterium tuberculosis transmission clusters. We carried out a thorough analysis of the epidemiological and bacteriological complexity of a cluster in Almería, Spain. The cluster, initially associated with Moroccan migrants and with no secondary cases identified in 4 years, then reappeared in Spanish-born individuals. In one case, two Mycobacterium tuberculosis clonal variants were identified. We reanalyzed the cluster, supported by the characterization of multiple cultured isolates and respiratory specimens, whole-genome sequencing, and epidemiological case interviews. Our findings showed that the cluster, which was initially thought to have restarted activity with just a single case harboring a small degree of within-host diversity, was in fact currently growing due to coincidental reactivation of past exposures, with clonal diversity transmitted throughout the cluster. In one case, within-host diversity was amplified, probably due to prolonged diagnostic delay. IMPORTANCE The precise study of the dynamics of tuberculosis transmission in socio-epidemiologically complex scenarios may require more thorough analysis than the standard molecular epidemiology strategies. Our study illustrates the epidemiological and bacteriological complexity present in a transmission cluster in a challenging epidemiological setting with a high proportion of migrant cases. The combination of whole-genome sequencing, refined and refocused epidemiological interviews, and in-depth analysis of the bacterial composition of sputa and cultured isolates was crucial in order to correctly reinterpret the true nature of this cluster. Our global approach allowed us to reinterpret correctly the unnoticed epidemiological and bacteriological complexity involved in the Mycobacterium tuberculosis transmission event under study, which had been overlooked by the usual molecular epidemiology approaches.
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Affiliation(s)
- Fermin Acosta
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Teresa Guerra-Galán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra R. Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Suppli CH, Norman A, Folkvardsen DB, Gissel TN, Weinreich UM, Koch A, Wejse C, Lillebaek T. First outbreak of multi-drug resistant tuberculosis (MDR-TB) in Denmark involving six Danish-born cases. Int J Infect Dis 2022; 117:258-263. [PMID: 35158061 DOI: 10.1016/j.ijid.2022.02.017] [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: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Denmark is a tuberculosis (TB) and multi-drug resistant (MDR) TB low-incidence country at 5 and 0.05 cases per 100.000 population, respectively. Until 2018, transmission of MDR-TB was nonexistent except for few pairwise related family-cases. In this study we describe the first MDR-TB outbreak in Denmark. METHODS Based on genotyping of all Mycobacterium tuberculosis (Mtb) culture-positive cases in Denmark spanning three decades, six molecular- and epidemiologically linked Danish-born cases were identified as the first cluster of MDR-TB in Denmark. The primary case was diagnosed posthumously in 2010 followed by five epidemiologically linked cases from 2018 through 2019. RESULTS AND CONCLUSION Through a combination of routine Mtb genotyping and clinical epidemiological surveillance data, we identified the first Danish MDR-TB outbreak spanning 10 years and were able to disclose the specific transmission pathways in detail guiding the outbreak investigations. The occurrence of an MDR-TB outbreak in a resource rich TB low incidence setting like Denmark, highlights the importance of a collaborative control system combining classical contact tracing; timely identification of drug resistant TB through rapid diagnostics; and a close collaboration between clinicians, classical- and molecular epidemiologists for the benefit of TB control.
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Affiliation(s)
- Camilla Hiul Suppli
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Tina Nørregaard Gissel
- Department of Internal Medicine, Region Hospital Viborg, Heibergs Alle 4F, DK-8800 Viborg, Denmark
| | - Ulla Møller Weinreich
- Department of Respiratory Diseases, Aalborg University Hospital, Aalborg, Mølleparkvej 4, DK-9000 Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Søndre Skovvej 15, DK-9000 Aalborg, Denmark
| | - Anders Koch
- Global Health Section, Department of Public Health, University of Copenhagen Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark; Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; Department of Infectious Diseases, Rigshospitalet University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Christian Wejse
- GloHAU, Center for Global Health, Dept of Public Health, Aarhus University, Bartholins Allé 2, DK-8000 Aarhus C, Denmark; Dept of Infectious Diseases, Institute for Clinical Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark; Global Health Section, Department of Public Health, University of Copenhagen Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
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Draft Genome Sequences of 77 Endemic Multidrug-Resistant Mycobacterium tuberculosis Strains of SIT41 (TUR) Spoligotype from Bulgaria. Microbiol Resour Announc 2022; 11:e0111121. [PMID: 35142538 PMCID: PMC8830331 DOI: 10.1128/mra.01111-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequences of multidrug-resistant (MDR) Mycobacterium tuberculosis strains are of particular interest to study the molecular mechanisms of drug resistance evolution. Here, we report the draft genome sequences of 77 endemic multidrug-resistant Mycobacterium tuberculosis strains of SIT41 (TUR) spoligotype from Bulgaria. SIT41 spoligotype is dominant (>40%) among the MDR-TB strains in Bulgaria.
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Kone B, Somboro AM, Kone M, Holl JL, Baya B, Dabitao D, Diallo D, Diarra B, Kone A, Sarro YDS, Sanogo M, Togo AC, Murphy RL, Diallo S, Coulibaly N, Camara F, Samake S, Diakite M, Doumbia S, Maiga M. Molecular epidemiology and genetic diversity of Mycobacterium tuberculosis complex in referral health centers of Bamako, Mali: What is new? Int J Infect Dis 2022; 117:204-211. [PMID: 35134562 PMCID: PMC9055845 DOI: 10.1016/j.ijid.2022.01.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background and Aims: Tuberculosis (TB) remains an important global health issue worldwide. Despite this scourge threatening many human lives, especially in developing countries, thus far, no advanced molecular epidemiology study using recent and more accurate tools has been conducted in Mali. Therefore, this study aimed to use variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) technology coupled with the spoligotyping method to accurately determine the hot spots and establish the epidemiological transmission links of TB in Bamako, Mali. Methods: In a cross-sectional study, 245 isolates of Mycobacterium tuberculosis complex (MTBC) were characterized using spoligotyping and MIRU-VNTR, and an epidemiological investigation was conducted. Results: Of the 245 isolates, 184 (75.1%) were formally identified. The most widespread strain was the Cameroon strain (83; 45.1%). Eight major clusters were identified: Ghana (27; 14.7%), West African 2 (22; 12%), Haarlem (13; 7.1%), H37Rv (t) (8; 4.3%), Latin American Mediterranean (8; 4.3%), and Uganda I and II (6; 3.3%). Statistical analysis showed a significant difference between lineages from the respective referral health centers of Bamako, Mali (P = 0.01). Conclusion: This study establishes, for the first time, an accurate spatial distribution of circulating MTB strains in Bamako, Mali. The data was used to identify strains and “hot spots” causing TB infection and can also be used for more targeted public health responses, particularly for hot spots of drug-resistant strains.
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Affiliation(s)
- Bourahima Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Anou M Somboro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahamadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Jane L Holl
- Center for Healthcare Delivery Science and Innovation, University of Chicago, Chicago, Illinois, USA
| | - Bocar Baya
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Dramane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Kone
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme Cg Togo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Robert L Murphy
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA
| | - Souleymane Diallo
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fatoumata Camara
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Samake
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamadou Diakite
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC) Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Biomedical Engineering Department, Northwestern University, Evanston, Illinois, USA.
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Micheni LN, Kassaza K, Kinyi H, Ntulume I, Bazira J. Detection of Mycobacterium tuberculosis multiple strains in sputum samples from patients with pulmonary tuberculosis in south western Uganda using MIRU-VNTR. Sci Rep 2022; 12:1656. [PMID: 35102181 PMCID: PMC8803872 DOI: 10.1038/s41598-022-05591-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Infections with multiple strains of Mycobacterium tuberculosis are now widely recognized as a common occurrence. Identification of patients infected with multiple strains provides both insight into the disease dynamics and the epidemiology of tuberculosis. Analysis of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats (MIRU-VNTR) has been shown to be highly sensitive in detecting multiple M. tuberculosis strains even in sputum. The goal of this study was to identify cases of multiple M. tuberculosis strain infections among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda and assessment of factors associated with multiple strain infections. DNA extracted directly from 78 sputum samples, each from an individual patient, was analyzed using the standard 24 loci MIRU-VNTR typing. Five (6.4%) of the 78 patients were infected with multiple strains of M. tuberculosis with all of them being the newly diagnosed cases while two-thirds of them were co-infected with HIV. Exact regression analysis projected that the natives were more likely to harbor multiple strains (OR; 0.981, 95% CI 0–7.926) as well as those with a high microbial load (OR; 0.390, 95% CI 0–3.8167). Despite these findings being not statistically significant due to the small sample size, this points to a critical component of disease dynamics that has clinical implications and emphasizes a need for a study using a larger cohort. It is also essential to study the potential factors associated with higher risk of exposure to newly diagnosed and HIV positive patients at the community level. In addition, our ability to detect multiple M. tuberculosis strains using the standard 24 loci MIRU-VNTR typing especially with allelic diversity in loci 2059 and 3171, which are excluded from the 15-locus MIRU-VNTR, lead us to recommend the use of this genotyping technique, especially in areas with tuberculosis endemicity similar to this study.
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Affiliation(s)
- Lisa Nkatha Micheni
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda. .,Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda.
| | - Kennedy Kassaza
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda
| | - Hellen Kinyi
- Department of Biochemistry, School of Medicine, Kabale University, Box 317, Kabale, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda.
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Couvin D, Cervera-Marzal I, David A, Reynaud Y, Rastogi N. SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis. Database (Oxford) 2022; 2022:6506437. [PMID: 35028657 PMCID: PMC8962452 DOI: 10.1093/database/baab081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022]
Abstract
Limited data are available for bovine tuberculosis and the infections it can cause in humans and other mammals. We therefore constructed a publicly accessible SITVITBovis database that incorporates genotyping and epidemiological data on Mycobacterium bovis. It also includes limited data on Mycobacterium caprae (previously synonymous with the name M. bovis subsp. Caprae) that can infect both animals and humans. SITVITBovis incorporates data on 25,741 isolates corresponding to 60 countries of origin (75 countries of isolation). It reports a total of 1000 spoligotype patterns: 537 spoligotype international types (SITs, containing 25 278 clinical isolates) and 463 orphan patterns, allowing a wide overview of the geographic distribution of various phylogenetical sublineages (BOV_1, BOV_2, BOV_3 and BOV_4-CAPRAE). The SIT identifiers of the SITVITBovis were compared to the SB numbers of the Mbovis.org database to facilitate crosscheck among databases. Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. Significant differences were observed when comparing age/gender of human isolates as well as various hosts. The database includes information on the regions where a strain was isolated as well as hosts involved, making it possible to see geographic trends. SITVITBovis is publicly accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis. Finally, a future second version is currently in progress to allow query of associated whole-genome sequencing data. Database URLhttp://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Iñaki Cervera-Marzal
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Audrey David
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Panaiotov S, Madzharov D, Hodzhev Y. Biodiversity of Mycobacterium tuberculosis in Bulgaria Related to Human Migrations or Ecological Adaptation. Microorganisms 2022; 10:microorganisms10010146. [PMID: 35056596 PMCID: PMC8778017 DOI: 10.3390/microorganisms10010146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/27/2023] Open
Abstract
Bulgaria is among the 18 high-priority countries of the WHO European Region with high rates of tuberculosis. The causative agent of tuberculosis is thought to have emerged in Africa 70,000 years ago, or during the Neolithic age, and colonized the world through human migrations. The established main lineages of tuberculosis correlate highly with geography. The goal of our study was to investigate the biodiversity of Mycobacteriumtuberculosis in Bulgaria in association with human migration history during the last 10 centuries. We analyzed spoligotypes and MIRU-VNTR genotyping data of 655 drug-sensitive and 385 multidrug-resistant M. tuberculosis strains collected in Bulgaria from 2008 to 2018. We assigned the genotype of all isolates using SITVITWEB and MIRU-VNTRplus databases and software. We investigated the major well-documented historical events of immigration to Bulgaria that occurred during the last millennium. Genetic profiles demonstrated that, with the exceptions of 3 strains of Mycobacterium bovis and 18 strains of Lineage 2 (W/Beijing spoligotype), only Lineage 4 (Euro-American) was widely diffused in Bulgaria. Analysis of well-documented immigrations of Roma from the Indian subcontinent during the 10th to the 12th centuries, Turkic peoples from Central Asia in the medieval centuries, and more recently Armenians, Russians, and Africans in the 20th century influenced the biodiversity of M. tuberculosis in Bulgaria but only with genotypes of sublineages within the L4. We hypothesize that these sublineages were more virulent, or that ecological adaptation of imported M. tuberculosis genotypes was the main driver contributing to the current genetic biodiversity of M. tuberculosis in Bulgaria. We also hypothesize that some yet unknown local environmental factors may have been decisive in the success of imported genotypes. The ecological factors leading to local genetic biodiversity in M. tuberculosis are multifactorial and have not yet been fully clarified. The coevolution of long-lasting pathogen hosts should be studied, taking into account environmental and ecological changes.
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Affiliation(s)
- Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
- Correspondence: ; Tel.: +359-887-720-061
| | | | - Yordan Hodzhev
- National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
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Belakehal F, Barth SA, Menge C, Mossadak HT, Malek N, Moser I. Evaluation of the discriminatory power of spoligotyping and 19-locus mycobacterial interspersed repetitive unit-variable number of tandem repeat analysis (MIRU-VNTR) of Mycobacterium bovis strains isolated from cattle in Algeria. PLoS One 2022; 17:e0262390. [PMID: 35015775 PMCID: PMC8751994 DOI: 10.1371/journal.pone.0262390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/23/2021] [Indexed: 11/19/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium (M.) bovis and M. caprae is a transmissible disease of livestock, notifiable to the World Organization for Animal Health (OIE). BTB particularly affects cattle and small ruminants and can be transmitted to humans thereby posing a significant threat to veterinary and public health worldwide. M. bovis is the principal cause of bTB in Algeria. In order to better understand the route of spreading and elaborate an eradication program, isolation and characterization of mycobacteria from Algerian cattle was performed. Sixty strains belonging to the M. tuberculosis complex were analyzed by spoligotyping, thereof 42 by 19-locus-MIRU-VNTR-typing. Spoligotyping revealed 16 distinguishable patterns (Hunter-Gaston discriminatory index [HGDI] of 0.8294), with types SB0120 (n = 20) and SB0121 (n = 13) being the most frequent patterns, representing 55% of the strains. Analyses based on 19-locus-MIRU-VNTR yielded 32 different profiles, five clusters and one orphan pattern, showing higher discriminatory power (HGDI = 0.9779) than spoligotyping. Seven VNTR-loci [VNTR 577 (alias ETR C), 2163b (QU11b), 2165 (ETR A), 2461 (ETR B), 3007 (MIRU 27), 2163a (QUB11a) and 3232 (QUB 3232)] were the most discriminative loci (HGDI ˃ 0.50). In conclusion, 19-locus-MIRU-VNTR yielded more information than spoligotyping concerning molecular differentiation of strains and better supports the elucidation of transmission routes of M. bovis between Algerian cattle herds.
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Affiliation(s)
- Faïza Belakehal
- High National Veterinary School, Laboratory of Food Hygiene and Quality Insurance System, El-Alia, Oued Smar, Algeria
- * E-mail: (FB); (SAB)
| | - Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- National Reference Laboratory for Bovine Tuberculosis, at Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- * E-mail: (FB); (SAB)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
| | - Hamdi T. Mossadak
- High National Veterinary School, Laboratory of Food Hygiene and Quality Insurance System, El-Alia, Oued Smar, Algeria
| | - Naïm Malek
- Central Military Hospital, Department of Microbiology, Kouba, Algeria
| | - Irmgard Moser
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
- National Reference Laboratory for Bovine Tuberculosis, at Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Germany
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Kikuchi T, Nakamura M, Hachisu Y, Hirai S, Yokoyama E. Molecular epidemiological analysis of Mycobacterium tuberculosis modern Beijing genotype strains isolated in Chiba Prefecture over 10 years. J Infect Chemother 2022; 28:521-525. [PMID: 35016826 DOI: 10.1016/j.jiac.2021.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/05/2021] [Accepted: 12/21/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The prevalence of the phylogenetic groups of Mycobacterium tuberculosis Beijing genotype has been reported to be similar in different areas of Japan. However, recent reports from rural areas of Japan show a low prevalence of modern Beijing strains, suggesting that the distribution of modern Beijing strains may have changed recently. Therefore, multi-locus variable number of tandem repeats analysis (MLVA) and draft whole genome sequence (DWGS) analysis were carried out to investigate the prevalence of particular genotype strains. METHODS Nine hundred and ninety modern Beijing strains were studied using minimum spanning tree (MST) analysis and neighbor-net analysis of MLVA and WGS data. RESULTS An MST of M. tuberculosis Beijing genotype strains reconstructed from 12 loci-MLVA data showed two large complexes with the J12-0006 MLVA pattern. In one of the complexes, strains with the pECT07 pattern produced by 24 loci-MLVA and its SLVs were most prevalent. DWGS analysis was carried out for pECT07 and its SLV strains. Neighbor-net and MST analyses of the DWGS data showed that pECT07 and its SLV strains were grouped in separate clusters. When all the combinations of two of the tested strains were analyzed, MST analysis showed that only 9 (1.7%) of the 528 pairs of tested strains had 5 or less SNPs. CONCLUSIONS The results of this study suggested that pECT07 and its variants were prevalent among M. tuberculosis modern Beijing strains in Chiba Prefecture, but the prevalence of those strains may not have been due to an earlier large-scale latent outbreak.
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Affiliation(s)
- Takashi Kikuchi
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan.
| | - Masaki Nakamura
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan
| | - Yushi Hachisu
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan; Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan
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Van Deun A, Bola V, Lebeke R, Kaswa M, Hossain MA, Gumusboga M, Torrea G, De Jong BC, Rigouts L, Decroo T. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac037. [PMID: 35415609 PMCID: PMC8994197 DOI: 10.1093/jacamr/dlac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
| | - Valentin Bola
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Rossin Lebeke
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Michel Kaswa
- Programme National de Lutte contre la Tuberculose, Direction Nationale, Kinshasa, République Démocratique du Congo
| | | | - Mourad Gumusboga
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Gabriela Torrea
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Bouke Catharine De Jong
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Tom Decroo
- Institute of Tropical Medicine, Unit of HIV and TB, Department of Clinical Sciences, 2000 Antwerp, Belgium
- Corresponding author. E-mail:
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Güven Gökmen T, Yakici G, Kalayci Y, Turut N, Meral Ocal M, Haligür M, Günaydin E, Köksal F. Molecular characterization of Mycobacterium bovis strains isolated from cattle and humans by spoligotyping and 24-locus MIRU-VNTR, and prevalence of positive IGRA in slaughterhouse workers in Southern Turkey. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:210-218. [PMID: 36425601 PMCID: PMC9681978 DOI: 10.22099/ijvr.2022.42580.6186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/09/2022] [Accepted: 06/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mycobacterium bovis is a zoonotic member of the Mycobacterium tuberculosis complex with a wide range of hosts, mainly cattle. Molecular epidemiological studies should be conducted to determine the transmission route, zoonotic risk factors, and phylogenetic relationships of M. bovis strains. Aims: This study aimed to characterize bovine and human M. bovis isolates by molecular methods. METHODS Molecular characterization and clonal relationship of strains isolated from tissue and organ samples of 76 cattle with positive tuberculin tests were collected from a slaughterhouse, and four M. bovis strains isolated from clinical materials of patients with suspected pulmonary TB isolates were analyzed using 24-locus MIRU-VNTR and spoligotyping methods. QuantiFERON-TB Gold Plus (QFT-Plus; Qiagen) was used to determine the prevalence of latent TB infection among 21 slaughterhouse personnel including 7 veterinarians, 12 butchers, 1 caretaker, and 1 veterinary technician. RESULTS SB0288/SIT685 type was detected in both cattle and humans by the spoligotyping method. When evaluating MIRU-VNTR, the presence of a 100% compatible pattern between human and bovine isolates was not detected, but some human samples were found to be 91.6% similar to a bovine sample. In addition, 21 slaughterhouse workers were screened with the interferon gamma-released assay (IGRA) and a 23.8% positivity was detected. CONCLUSION Clonal similarity was determined between the bovine and human isolates using the MIRU-VNTR and spoligotyping methods and IGRA positivity in the occupational group suggested that M. bovis might be associated with pulmonary tuberculosis in humans.
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Affiliation(s)
- T. Güven Gökmen
- Department of Microbiology, Ceyhan Veterinary Faculty, Cukurova University, 01330, Adana, Turkey
| | - G. Yakici
- Tuberculosis Region Laboratory, Tropical Disease and Research Center, Cukurova University, 01330, Adana, Turkey
| | - Y. Kalayci
- Microbiology Laboratory, Adana City Hospital, 01230, Adana, Turkey
| | - N. Turut
- MSc, Microbiology Laboratory, Adana Veterinary Control Institute, 01250, Adana, Turkey
| | - M. Meral Ocal
- Department of Microbiology, Medicine Faculty, Cukurova University, 01330, Adana, Turkey
| | - M. Haligür
- Department of Pathology, Ceyhan Veterinary Faculty, Cukurova University, 01330, Adana, Turkey
| | - E. Günaydin
- Department of Microbiology, Veterinary Faculty, Kastamonu University, 37150, Kastamonu, Turkey
| | - F. Köksal
- Department of Microbiology, Medicine Faculty, Cukurova University, 01330, Adana, Turkey
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Asadi L, Croxen M, Heffernan C, Dhillon M, Paulsen C, Egedahl ML, Tyrrell G, Doroshenko A, Long R. How much do smear-negative patients really contribute to tuberculosis transmissions? Re-examining an old question with new tools. EClinicalMedicine 2022; 43:101250. [PMID: 35036885 PMCID: PMC8743225 DOI: 10.1016/j.eclinm.2021.101250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sputum smear microscopy is a common surrogate for tuberculosis infectiousness. Previous estimates that smear-negative patients contribute 13-20% of transmissions and are, on average, 20 to 25% as infectious as smear-positive cases are understood to be high. Herein, we use an ideal real-world setting, a comprehensive dataset, and new high-resolution techniques to more accurately estimate the true transmission risk of smear-negative cases. METHODS We treated all adult culture-positive pulmonary TB patients diagnosed in the province of Alberta, Canada from 2003 to 2016 as potential transmitters. The primary data sources were the Alberta TB Registry and the Provincial Laboratory for Public Health. We measured, as primary outcomes, the proportion of transmissions attributable to smear-negative sources and the relative transmission rate. First, we replicated previous studies by using molecular (DNA) fingerprint clustering. Then, using a prospectively collected registry of TB contacts, we defined transmission events as active TB amongst identified contacts who either had a 100% DNA fingerprint match to the source case or a clinical diagnosis. We supplemented our analysis with genome sequencing on temporally and geographically linked DNA fingerprint clusters of cases not identified as contacts. FINDINGS There were 1176 cases, 563 smear-negative and 613 smear-positive, and 23,131 contacts. Replicating previous studies, the proportion of transmissions attributable to smear-negative source cases was 16% (95% CI, 12-19%) and the relative transmission rate was 0.19 (95% CI, 0.14-0.26). With our combined approach, the proportion of transmission was 8% (95% CI, 3-14%) and the relative transmission rate became 0.10 (95% CI, 0.05-0.19). INTERPRETATION When we examined the same outcomes as in previous studies but refined transmission ascertainment with the addition of conventional epidemiology and genomics, we found that smear-negative cases were ∼50% less infectious than previously thought. FUNDING Alberta Innovates Health Solutions.
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Affiliation(s)
- Leyla Asadi
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Matthew Croxen
- The Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Courtney Heffernan
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Mannat Dhillon
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Catherine Paulsen
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Mary Lou Egedahl
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Greg Tyrrell
- The Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Alexander Doroshenko
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Richard Long
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
- Corresponding author.
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Singh J, Singh N, Suresh G, Srivastava R, Aggarwal U, Behera D, Munisamy M, Malhotra AG, Singh S. A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients. Front Cell Infect Microbiol 2022; 12:953443. [PMID: 36310875 PMCID: PMC9597297 DOI: 10.3389/fcimb.2022.953443] [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: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
SETTING Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. OBJECTIVES We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. PATIENTS AND METHODS Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. RESULTS A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. CONCLUSION The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
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Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Gayatri Suresh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Rahul Srivastava
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Upasna Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Digamber Behera
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
- Department of Pulmonary Medicine, PGIMER, Chandigarh, India
| | - Murali Munisamy
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | | | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
- Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
- *Correspondence: Sarman Singh, ;
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Du J, Li Q, Liu M, Wang Y, Xue Z, Huo F, Zhang X, Shang Y, Li S, Huang H, Pang Y. Distinguishing Relapse From Reinfection With Whole-Genome Sequencing in Recurrent Pulmonary Tuberculosis: A Retrospective Cohort Study in Beijing, China. Front Microbiol 2021; 12:754352. [PMID: 34956119 PMCID: PMC8693897 DOI: 10.3389/fmicb.2021.754352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Tuberculosis recurrence is still a major problem for the control of tuberculosis, and the cause of the recurrence is still unclear. Methods: We retrospectively recruited 68 pairs of samples of Mycobacterium tuberculosis (MTB) from recurrent TB cases in Beijing Chest Hospital between January 2008 and December 2019. The whole-genome sequencing was conducted to analyze single-nucleotide polymorphism (SNP) and to identify whether recurrent disease was due to relapse or reinfection. The BACTEC MGIT was performed to compare differences in drug susceptibility profiles between two episodes. Results: 62 (91.2%) out of 68 confirmed recurrence were due to relapse, whereas the remaining six (8.8%) were due to reinfection. And there was a strong association between earlier relapse and underlying chronic diseases. In addition, the MTB isolates from non-diabetic patients had a higher mutation rate than those from diabetic patients. A community transmission was also identified in our cohort. Levofloxacin resistance was the most frequently observed drug resistance for 12.9% relapse cases. Conclusion: The relapse of a previous episode in Beijing. The underlying chronic diseases are associated with an earlier TB relapse. MTB isolates were more prone to develop levofloxacin resistance than moxifloxacin resistance after FQ exposure. The patients at high-risk for relapses deserve more careful investigation.
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Affiliation(s)
- Jian Du
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qing Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Min Liu
- Provincial Center for Tuberculosis Control and Prevention, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Yufeng Wang
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Zhongtan Xue
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia. Antibiotics (Basel) 2021; 11:antibiotics11010029. [PMID: 35052906 PMCID: PMC8773284 DOI: 10.3390/antibiotics11010029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Globally, tuberculosis (TB) is a major cause of death due to antimicrobial resistance. Mycobacterium tuberculosis CAS1-Kili strains that belong to lineage 3 (Central Asian Strain, CAS) were previously implicated in the spread of multidrug-resistant (MDR)-TB in Lusaka, Zambia. Thus, we investigated recent transmission of those strains by whole-genome sequencing (WGS) with Illumina MiSeq platform. Twelve MDR CAS1-Kili isolates clustered by traditional methods (MIRU-VNTR and spoligotyping) were used. A total of 92% (11/12) of isolates belonged to a cluster (≤12 SNPs) while 50% (6/12) were involved in recent transmission events, as they differed by ≤5 SNPs. All the isolates had KatG Ser315Thr (isoniazid resistance), EmbB Met306 substitutions (ethambutol resistance) and several kinds of rpoB mutations (rifampicin resistance). WGS also revealed compensatory mutations including a novel deletion in embA regulatory region (−35A > del). Several strains shared the same combinations of drug-resistance-associated mutations indicating transmission of MDR strains. Zambian strains belonged to the same clade as Tanzanian, Malawian and European strains, although most of those were pan-drug-susceptible. Hence, complimentary use of WGS to traditional epidemiological methods provides an in-depth insight on transmission and drug resistance patterns which can guide targeted control measures to stop the spread of MDR-TB.
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72
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Shrestha A, Picoy J, Torres A, Moore DA, Gilman RH, Coronel J, Grandjean L. A case report of transmission and disease caused by Mycobacterium caprae and Mycobacterium bovis in Lima, Peru. BMC Infect Dis 2021; 21:1265. [PMID: 34930187 PMCID: PMC8686613 DOI: 10.1186/s12879-021-06944-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Tuberculosis (TB) burden in Peru is significant with respect to both disease morbidity and mortality. Furthermore the recent diversification of farming enterprise to include a wide range of animal species has necessitated the consideration of members of the Mycobacterium Tuberculosis Complex (MTBC) with the potential for zoonotic transmission. M. bovis and M. caprae, a lesser known member of the MTBC exhibit an exceptionally wide host spectrum in animals and are capable of causing disease in humans. M. bovis has a predictable resistance profile which includes resistance to pyrazinamide. Thus, failure to identify M. bovis as the causative agent in reported TB cases leads to higher levels of treatment failure and contributes to the transmission of drug-resistant TB. CASE PRESENTATION Reported here are the clinical presentations, investigations and treatment histories of two patients identified from a population level genotyping study in Lima, Peru that were at the time of treatment thought to be M. tuberculosis patients but in retrospect were spectated using whole genome sequencing as M. caprae and M. Bovis. CONCLUSIONS The cases reported here constitute convincing evidence that M. caprae and M. bovis are causative agents of TB infection in humans in Peru and underscore the importance of species-level MTBC member identification to effectively control and treat zoonotic TB. Furthermore these cases highlight the challenges of using clinical risk factors to identify cases of zoonotic TB in humans as their clinical presentation and transmission history is often difficult to distinguish from anthroponotic TB.
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Affiliation(s)
- Amber Shrestha
- grid.420468.cDepartment of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH UK
| | - Janeth Picoy
- Department of Infectious Disease, Diresa Callao Jr, Colina #879, Bellavista, 07016 Lima, Peru
| | - Arturo Torres
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, South Kensington, London, SW7 2AZ UK
| | - David A. Moore
- grid.8991.90000 0004 0425 469XTB Centre, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Robert H. Gilman
- grid.11100.310000 0001 0673 9488Laboratorio de Tuberculosis, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru ,grid.21107.350000 0001 2171 9311Department of International Health, School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia: Lima, Lima, Peru
| | - Louis Grandjean
- Department of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK. .,University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK.
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73
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Asgharzadeh M, Taghinejad Z, Mahdavipoor B, Asgharzadeh V, Kafil HS, Rashedi J. Mixed tuberculosis infections in Northwest of Iran. LE INFEZIONI IN MEDICINA 2021; 29:583-588. [PMID: 35146368 PMCID: PMC8805470 DOI: 10.53854/liim-2904-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/17/2021] [Indexed: 06/14/2023]
Abstract
Primary Mycobacterium tuberculosis (MTB) infection doesn't provide protection against secondary infection and patients can suffer from multiple strains of M. tuberculosis simultaneously. The aim of this study was to use molecular genotyping to identify cases of mixed infection in Northwest of Iran. One hundred and twenty-one positive culture isolates of M. tuberculosis were prepared from patients consecutively in Northwest of Iran from March 2017 to March 2018 and then microevolution and mix infection were assessed using the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. MIRU-VNTR analysis revealed that nine samples (7.3%) had double alleles in at least one locus, as observed by five cases of microevolution, and four cases (3.3%) of mixed infection. According to this study, mixed infection in Northwest of Iran has significantly decreased compared to 13 years ago (7.1% decreased to 3.3%), and in order to eradicate tuberculosis it is necessary to identify all cases of mixed infection, at least in recurrent cases, in the future.
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Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center and Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Taghinejad
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Asgharzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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74
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Rudeeaneksin J, Klayut W, Srisungngam S, Bunchoo S, Toonkomdang S, Wongchai T, Chuenchom N, Phetsuksiri B. Putative extensive and pre-extensive drug resistant-tuberculosis associated with unusual genotypes on the Thailand-Myanmar border. Rev Inst Med Trop Sao Paulo 2021; 63:e85. [PMID: 34878043 PMCID: PMC8660029 DOI: 10.1590/s1678-9946202163085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Extensive drug-resistant tuberculosis (XDR-TB) is highly life threatening and its
diagnosis is usually difficult and time-consuming. Here we present the first two
cases of XDR and pre-XDR-TB diagnosed in 2018 on the Thailand-Myanmar border,
more specifically in Tak province. Rapid detection of XDR-TB was performed by
loop-mediated isothermal amplification (LAMP), Xpert MTB/RIF, and line probe
assays. Mutation analyses targeting rpoB,
katG, inhA, gyrA and
rrs genes showed an association with drug-resistant
phenotypes, except for rifampicin resistance. Spoligotyping revealed uncommon
Beijing and T2 genotypes and the analysis of M. tuberculosis
interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) showed
the presence of more polymorphisms. This report highlights the importance of the
early detection of drug-resistant tuberculosis by molecular tests followed by
phenotyping assays. Based on the up-to-date definition of XDR- and pre-XDR-TB,
the susceptibility testing for bedaquiline and linezolid is required and the two
reported cases may correspond to putative XDR-TB.
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Affiliation(s)
- Janisara Rudeeaneksin
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Wiphat Klayut
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sopa Srisungngam
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Supranee Bunchoo
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | | | | | - Benjawan Phetsuksiri
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.,Ministry of Public Health, Medical Sciences Technical Office, Department of Medical Sciences, Nonthaburi, Thailand
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75
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Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Front Genet 2021; 12:683515. [PMID: 34858467 PMCID: PMC8630622 DOI: 10.3389/fgene.2021.683515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.
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Affiliation(s)
- Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bekzat Toksanbayeva
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Anar Rakisheva
- Department of Phthisiopulmonology, School of General Medicine, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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76
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María Irene CC, Juan Germán RC, Gamaliel LL, Dulce Adriana ME, Estela Isabel B, Brenda Nohemí M, Payan Jorge B, Zyanya Lucía ZB, Myriam BDV, Fernanda CG, Adrian OL, Martha Isabel M, Rogelio HP. Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: a perspective from the transcriptome. Virulence 2021; 12:1689-1704. [PMID: 34228582 PMCID: PMC8265813 DOI: 10.1080/21505594.2021.1936432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including Nkiras, Dleu2, and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.
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Affiliation(s)
- Cerezo-Cortés María Irene
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | | | - López-Leal Gamaliel
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mata-Espinosa Dulce Adriana
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bini Estela Isabel
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Marquina–Casitllo Brenda Nohemí
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Barrios Payan Jorge
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Zatarain-Barrón Zyanya Lucía
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bobadilla del Valle Myriam
- Departamento De Microbiología Clínica, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán Ciudad De México, México
| | - Cornejo-Granados Fernanda
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Ochoa-Leyva Adrian
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Murcia Martha Isabel
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | - Hernández-Pando Rogelio
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
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77
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Zenteno-Cuevas R, Munro-Rojas D, Pérez-Martínez D, Fernandez-Morales E, Jimenez-Ruano AC, Montero H, Escobar L, de Igartua E, Trigos Á, Fuentes-Dominguez J. Genetic diversity and drug susceptibility of Mycobacterium tuberculosis in a city with a high prevalence of drug resistant tuberculosis from Southeast of Mexico. BMC Infect Dis 2021; 21:1202. [PMID: 34847856 PMCID: PMC8630842 DOI: 10.1186/s12879-021-06904-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background Mexico is on the top five countries with the highest number of TB cases in America continent, nevertheless, information about genotypes circulating is practically unknown. Considering the above this study aims to characterize the genetic diversity of TB in the city of Veracruz, México. Methods A cross-sectional study was conducted among positive smear samples from patients living in Veracruz City, samples were cultured, and first-line drug profiles determined. Genotyping was made by spoligotyping and MIRU-VNTR 24 loci. Associations of lineages, clusters, and variables were also analyzed. Results Among the 202 isolates analyzed resistance to at least one drug was observed in 60 (30%) isolates and 41(20%) were multidrug-resistant. Three major lineages were identified: L4/Euro-American (88%), L1/Indo-Oceanic (9%), and L2/East Asian (3%). The Euro-American lineage included more than six sublineages, the most abundant were: H (32%), T (23%), LAM (18%), and X (12%). 140 isolates (70%) were placed in 42 SITs patterns. Conclusions These results provide the first baseline data on the genetic structure of TB in the city of Veracruz. Sublineages H, X and LAM were predominant; however, it was founded an important diversity of genotypes that could contribute to the dispersion of TB and explain the high prevalence. This information might be useful for the development of further interventions to reduce impact of TB. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06904-z.
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Affiliation(s)
- Roberto Zenteno-Cuevas
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México. .,Multidisciplinary Research Network on Tuberculosis, Veracruz, Mexico.
| | | | - Damián Pérez-Martínez
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México.,Doctorate in Health Sciences Program, Health Sciences Institute, University of Veracruz, Veracruz, Mexico
| | - Esdras Fernandez-Morales
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México.,Master of Health Science Program, Health Sciences Institute, University of Veracruz, Xalapa, Veracruz, Mexico
| | - Ana C Jimenez-Ruano
- Master of Health Science Program, Health Sciences Institute, University of Veracruz, Xalapa, Veracruz, Mexico
| | - Hilda Montero
- Public Health Institute, University of Veracruz, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Ánimas, Xalapa, 91190, Veracruz, México
| | | | | | - Ángel Trigos
- Research Center in Applied Mycology, University of Veracruz, Xalapa, Veracruz, Mexico
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78
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Bonnet I, Enouf V, Morel F, Ok V, Jaffré J, Jarlier V, Aubry A, Robert J, Sougakoff W. A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB ® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples. Front Cell Infect Microbiol 2021; 11:707244. [PMID: 34778100 PMCID: PMC8586210 DOI: 10.3389/fcimb.2021.707244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.
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Affiliation(s)
- Isabelle Bonnet
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Enouf
- Plateforme de Microbiologie Mutualisée (P2M), Pasteur International Bioresources network (PIBnet), Institut Pasteur, Paris, France
| | - Florence Morel
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vichita Ok
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérémy Jaffré
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Vincent Jarlier
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France
| | - Alexandra Aubry
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Jérôme Robert
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
| | - Wladimir Sougakoff
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, France.,Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, France.,Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, France
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Practical approach to detection and surveillance of emerging highly resistant Mycobacterium tuberculosis Beijing 1071-32-cluster. Sci Rep 2021; 11:21392. [PMID: 34725411 PMCID: PMC8560753 DOI: 10.1038/s41598-021-00890-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022] Open
Abstract
Ancient sublineage of the Mycobacterium tuberculosis Beijing genotype is endemic and prevalent in East Asia and rare in other world regions. While these strains are mainly drug susceptible, we recently identified a novel clonal group Beijing 1071-32 within this sublineage emerging in Siberia, Russia and present in other Russian regions. This cluster included only multi/extensive drug resistant (MDR/XDR) isolates. Based on the phylogenetic analysis of the available WGS data, we identified three synonymous SNPs in the genes Rv0144, Rv0373c, and Rv0334 that were specific for the Beijing 1071-32-cluster and developed a real-time PCR assay for their detection. Analysis of the 2375 genetically diverse M. tuberculosis isolates collected between 1996 and 2020 in different locations (European and Asian parts of Russia, former Soviet Union countries, Albania, Greece, China, Vietnam, Japan and Brazil), confirmed 100% specificity and sensitivity of this real-time PCR assay. Moreover, the epidemiological importance of this strain and the newly developed screening assay is further stressed by the fact that all identified Beijing 1071-32 isolates were found to exhibit MDR genotypic profiles with concomitant resistance to additional first-line drugs due to a characteristic signature of six mutations in rpoB450, rpoC485, katG315, katG335, rpsL43 and embB497. In conclusion, this study provides a set of three concordant SNPs for the detection and screening of Beijing 1071-32 isolates along with a validated real-time PCR assay easily deployable across multiple settings for the epidemiological tracking of this significant MDR cluster.
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80
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Chan TH, Huang CS, Tu C, Jou R. Bovine tuberculosis in Taiwan, 2008-2019. Transbound Emerg Dis 2021; 69:e814-e822. [PMID: 34724711 DOI: 10.1111/tbed.14371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/22/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB) is a zoonosis caused by Mycobacterium bovis. The impact of bTB on global TB control has been underestimated. We adopted the One Health approach to human bTB surveillance in Taiwan. Of 20,972 human TB cases, 202 (1.0%) were bTB, 78.2% were in males, 85.1% were new cases, 83.2% were pulmonary TB, and most were in Central (52.5%) and Southern (24.8%) Taiwan. Only 18.8% of bTB patients had known animal contact. Of the 202 human M. bovis strains, 100% were resistant to pyrazinamide (PZA), 30.2% were concurrently resistant to isoniazid (INH) and 2.0% were multidrug resistant, defined as being resistant to at least INH and rifampin. Whereas, of the 22 animal M. bovis strains, 100% and 22.7% were resistant to PZA and INH, respectively. Seven spoligotypes and 25 mycobacterial interspersed repetitive unit genotypes were identified. The predominant genotype, SB0265, was also prevalent in livestock. Notably, six animal-specific M. bovis genotypes were identified. bTB differential diagnosis and drug resistance detection are crucial for TB control. Comprehensive surveillance and human-animal interface investigations are needed.
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Affiliation(s)
- Tai-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chun-Sheng Huang
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, New Taipei City, Taiwan, ROC
| | - Chien Tu
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, New Taipei City, Taiwan, ROC
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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81
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Li H, Liu C, Liang M, Liu D, Zhao B, Shi J, Zhao Y, Ou X, Zhang G. Tuberculosis Outbreak in an Educational Institution in Henan Province, China. Front Public Health 2021; 9:737488. [PMID: 34712640 PMCID: PMC8545879 DOI: 10.3389/fpubh.2021.737488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
On June 17, 2018, a case of pulmonary tuberculosis (TB) was reported among students at a senior high school in Luoning, China. The outbreak encompassed a total of 23 cases along with TB screening in the whole school by means of PPD and chest X-ray. By the end of September 2018, the entire 9 cases cultured positive had epidemiological association. All of the 9 Mycobacterium tuberculosis (Mtb) isolates available were sensitive to all drugs tested and had similar spoligotyping and 15 loci mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profile. Whole-genome sequencing (WGS) of the Mtb isolates revealed 20 variable nucleotide positions within 8 cases, indicating a clonal outbreak. The index case, which was first identified and diagnosed, is separated from the cluster by a minimum number of 95 distinct SNPs. Minimum distance spanning tree (MST) indicted that the 8 cases were indeed part of a single transmission chain. It was concluded that this is an epidemic situation of TB outbreak exposed by the aggrieved index case at school, which was caused by the veiled infectious case wherein a student was suffering from TB and attending school simultaneously.
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Affiliation(s)
- Hui Li
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Liang
- Luoyang Center for Disease Control and Prevention, Luoyang, China
| | - Dongxin Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Shi
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guolong Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
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82
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de Melo EH, Gomes HM, Suffys PN, Lopes MQP, de Figueiredo Teixeira RL, Dos Santos ÍR, Franco MMJ, Langoni H, Paes AC, Afonso JAB, de Mendonça CL. Genotypic Characterization of Mycobacterium bovis Isolates From Dairy Cattle Diagnosed With Clinical Tuberculosis. Front Vet Sci 2021; 8:747226. [PMID: 34708105 PMCID: PMC8542897 DOI: 10.3389/fvets.2021.747226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Molecular diagnosis of bovine tuberculosis plays an essential role in the epidemiological knowledge of the disease. Bovine tuberculosis caused by Mycobacterium bovis represents a risk to human health. This study aimed to perform the genotypic characterization of M. bovis isolated from bovines diagnosed as tuberculosis from dairy herds in the state of Pernambuco, Brazil. Granulomas from 30 bovines were sent for microbiological culture, and colonies compatible with Mycobacterium spp. were obtained in at least one culture from 17/30 granulomas. All isolates were confirmed to be M. bovis by spoligotyping and 24loci MIRU-VNTR typing. While spoligotyping characterized the isolates as SB0121, SB0295, SB0852, SB0120, and an unclassified genotype, 24loci MIRU-VNTR rendered two clusters of two isolates each and 13 unique profiles. Loci ETR-A showed higher discriminatory power, and loci (ETR-B, ETR-C, MIRU16, MIRU27, and QUB26) showed moderate allelic diversity. This is the first study on the genetic variability of the infectious agent cause of bovine TB in Pernambuco and demonstrates variability of strains in the state. Thus, it corroborates the importance of this microorganism as agent of bovine tuberculosis and its zoonotic potential, this epidemiological tool being a determinant in the rigor of the sanitary practices of disease control in dairy herds.
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Affiliation(s)
| | - Harrison Magdinier Gomes
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Márcia Quinhones Pires Lopes
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Raquel Lima de Figueiredo Teixeira
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Ícaro Rodrigues Dos Santos
- Laboratório de Biologia Molecular Aplicada à Micobactérias, Fundação Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada à Micobactérias, Rio de Janeiro, Brazil
| | - Marília Masello Junqueira Franco
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | - Helio Langoni
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | - Antonio Carlos Paes
- Departamento de Higiene Veterinária e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Carla Lopes de Mendonça
- Clínica de Bovinos de Garanhuns, Universidade Federal Rural de Pernambuco, Garanhuns, Brazil
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83
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Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021; 114:142-150. [PMID: 34718155 DOI: 10.1016/j.ijid.2021.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Zambia is among the 30 high tuberculosis burden countries in the world. Despite increasing reports of multidrug resistant tuberculosis (MDR-TB) in routine surveillance, information on the transmission of MDR Mycobacterium tuberculosis strains is largely unknown. This study elucidated genetic diversity and transmission of MDR M. tuberculosis strains in Lusaka, Zambia. METHODS Eighty-five MDR M. tuberculosis samples collected from the year 2013 to 2017 at the University Teaching Hospital were used. Drug-resistance associated gene sequencing, spoligotyping, 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats, and multiplex PCR for RD-Rio sub-lineage identification were applied. RESULTS Clades identified were LAM (48%), CAS (29%), T (14%), X (6%) and Harlem (2%). Strains belonging to SITs 21/CAS1-Kili and 20/LAM1 formed the largest clonal complexes. Combined spoligotyping and 24 loci-MIRU-VNTR revealed 47 genotypic patterns with clustering rate of 63%. Ninety five percent of LAM strains belonged to RD-Rio sub-lineage. CONCLUSION The high clustering rate suggested that a large proportion of MDR-TB was due to recent transmission rather than independent acquisition of MDR. This spread was attributed to clonal expansion of SIT21/CAS1-Kili and SIT20/LAM1 strains. Therefore, TB control programs recommending genotyping coupled with conventional epidemiological methods can guide measures for stopping the spread of MDR-TB.
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84
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Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2021; 131:102137. [PMID: 34673379 DOI: 10.1016/j.tube.2021.102137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022]
Abstract
Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.
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85
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Ushtanit A, Mikhailova Y, Lyubimova A, Makarova M, Safonova S, Filippov A, Borisov S, Zimenkov D. Genetic Profile of Linezolid-Resistant M. tuberculosis Clinical Strains from Moscow. Antibiotics (Basel) 2021; 10:antibiotics10101243. [PMID: 34680823 PMCID: PMC8532644 DOI: 10.3390/antibiotics10101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Linezolid, bedaquiline, and newer fluoroquinolones are currently placed as priority Group A drugs for the treatment of drug-resistant tuberculosis. The number of reported linezolid-resistant clinical strains is still low, and the correlation of molecular determinants with phenotype is not perfect. Methods: We determined the linezolid MICs for clinical isolates from the Moscow region and identified mutations in rplC and rrl genes. Results: All 16 linezolid-resistant isolates had previously reported mutations in the rplC or rrl loci, and 13 of them bore a RplC C154R substitution. Detection of this substitution in a heteroresistant state was not successful, probably, due to the more stable DNA secondary structure of the mutated fragment, which precludes its amplification in mixes with the wild-type DNA. Strains with an rplC mutation had higher linezolid MIC compared to isolates with rrl mutations. Conclusions: Linezolid resistance mostly emerged during treatment with the latest regimen. Three primary cases with linezolid resistance question the possible transmission of totally drug-resistant tuberculosis in the Moscow region, which demands further investigation.
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Affiliation(s)
- Anastasia Ushtanit
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Yulia Mikhailova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexandra Lyubimova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Marina Makarova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Svetlana Safonova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexey Filippov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Sergey Borisov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
- Correspondence:
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86
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Lin S, Wei S, Zhao Y, Dai Z, Lin J, Pang Y. Genetic Diversity and Drug Susceptibility Profiles of Multidrug-Resistant Tuberculosis Strains in Southeast China. Infect Drug Resist 2021; 14:3979-3989. [PMID: 34611415 PMCID: PMC8487280 DOI: 10.2147/idr.s331516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 11/23/2022] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) isolates collected from Fujian province, China were assessed for molecular epidemiological characteristics. Analysis of isolate genotype profiles revealed that the Beijing genotype was associated with especially high drug resistance and community transmission rates. Methods A total of 119 MDR-TB isolates obtained from TB patients in Fujian province were typed using 24–locus mycobacterium interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and spoligotyping. Drug susceptibility testing of all isolates was conducted using the L-J proportion method, with pyrazinamide (PZA) susceptibility testing conducted using the Mycobacterium Growth Indicator Tube System 960 (MGIT 960). Results We obtained 26 spoligotypes for the 119 isolates examined in this work. Spoligotyping results revealed that 80 (67.2%) isolates possessed the Beijing family genotypic profiles. Patients aged 25–44 years and ≥45 years were most likely to be infected by non-Beijing genotypes. The percentage of clustered cases with both PZA and ofloxacin (OFLX) resistance was significantly greater than the corresponding percentage for non-clustered cases. Of 44 PZA-resistant isolates, 28 isolates (63.6%) harbored pncA mutations, while pncA mutations were only detected in 7 (9.3%) PZA-susceptible isolates. Conclusion Our data demonstrate that the Beijing genotype is the dominant lineage among MDR-TB strains circulating in Fujian. Thus, MDR-TB infections occurring within this province are not likely associated with recent transmission events. PZA and fluoroquinolone resistance profiles were found to be associated with clustered isolates. Mutation of pncA is the main driver of MDR-TB PZA resistance and is associated with mutation sites scattered throughout the entire pncA protein-coding region.
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Affiliation(s)
- Shufang Lin
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People's Republic of China
| | - Shuzhen Wei
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People's Republic of China
| | - Yong Zhao
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People's Republic of China
| | - Zhisong Dai
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People's Republic of China
| | - Jian Lin
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou, People's Republic of China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
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87
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Long R, Lau A, Egedahl ML, Paulsen C, Heffernan C, Edwards B, Cooper R. Local Transmission Plays No Important Role in the Occurrence of Multidrug-Resistant Tuberculosis in Immigrants to Canada: An In-depth Epidemiologic Analysis. J Infect Dis 2021; 224:1029-1038. [PMID: 33502538 DOI: 10.1093/infdis/jiab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) tuberculosis has increased among migrants in Canada. The cause(s) of this increase is unknown. METHODS We performed a retrospective cohort study in a Canadian province with substantially increased immigration between 1982-2001 and 2002-2019. The proportion of MDR tuberculosis among migrants arriving from high MDR (HMDR) tuberculosis burden countries during these 2 periods was used to estimate the proportion of cases due to immigration versus change in proportion in the country of birth. Epidemiologic, spatiotemporal, and drug resistance pattern data were used to confirm local transmission. RESULTS Fifty-two of 3514 (1.48%) foreign-born culture-positive tuberculosis patients had MDR tuberculosis: 8 (0.6%) in 1982-2001 and 44 (2.0%) in 2002-2019. Between time periods, the proportion of MDR tuberculosis among migrants with tuberculosis from HMDR tuberculosis countries increased from 1.11% to 3.62%, P = .003; 31.6% attributable to recent immigration and 68.4% to a higher proportion of MDR tuberculosis in cases arrived from HMDR tuberculosis countries. No cases of MDR tuberculosis were attributable to local transmission. CONCLUSIONS In stark contrast to HMDR tuberculosis countries, local transmission plays no important role in the occurrence of MDR tuberculosis in Canada. Improved tuberculosis programming in HMDR tuberculosis countries is urgently needed.
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Affiliation(s)
- Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Angela Lau
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Catherine Paulsen
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Brett Edwards
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ryan Cooper
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Uddin MKM, Ather MF, Rahman A, Nasrin R, Rahman SMM, Kabir S, Chedid C, Ahmed S, Banu S. Genetic diversity and characterization of M. tuberculosis isolates causing extrapulmonary tuberculosis in Bangladesh. INFECTION GENETICS AND EVOLUTION 2021; 95:105052. [PMID: 34454121 DOI: 10.1016/j.meegid.2021.105052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) remains one of the leading causes of death and Bangladesh ranks 7th among the highest TB burden countries. Though molecular epidemiological data for pulmonary TB (PTB) have previously been described in Bangladesh, data on the molecular characterization and clinical association with different lineages among extrapulmonary TB (EPTB) is lacking. The aim of the study was to investigate the molecular characterization and lineage distribution of M. tuberculosis isolates obtained from patients with EPTB in Bangladesh. Between November 2015 and March 2017, a total of 1,340 EPTB specimens including lymph node, pus, tissue, ascitic fluid, cerebrospinal fluid, pleural fluid, abscess wall, urine etc. were collected from four tertiary care hospitals in Dhaka city, Bangladesh. Among the specimens, 141 were found positive on solid culture. Molecular characterization of the 141 isolates was done by deletion analysis, spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTR) analysis. Among the 141 isolates, 80 (56.7%) were found as 'modern' and the remaining 61 (43.3%) were 'ancestral' type. Spoligotyping results revealed 91 distinct patterns of which 74 isolates were unique and the remaining 67 were divided into 17 distinct clusters. East African- Indian (EAI) lineage was the most predominant, comprising 26 (18.4%) isolates, followed by the Beijing lineage (14.2%). 15-loci MIRU-VNTR analysis revealed that 132 isolates (93.5%) had unique patterns, whereas only 9 (6.5%) isolates were grouped into 4 distinct clusters. In conclusion, the study findings provide a first insight into genetic diversity of EPTB isolates in Bangladesh. The present study demonstrated that 'modern' strains were more prevalent among the EPTB cases, while EAI lineages were predominantly circulating in this region.
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Affiliation(s)
| | - Md Fahim Ather
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
| | - Arfatur Rahman
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh; Medicinal Chemistry Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Rumana Nasrin
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
| | - S M Mazidur Rahman
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
| | - Senjuti Kabir
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
| | - Carole Chedid
- Laboratoire des Pathogènes Emergents Centre International de Recherche en Infectiologie, 21 Avenue Tony Garnier, 69365 Lyon Cedex 07, France; Département de Biologie, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Shahriar Ahmed
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
| | - Sayera Banu
- Infectious Diseases Division, icddr,b 68, Shaheed Tajuddin Ahmed Sarani, Dhaka 1212, Bangladesh.
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Fitzgibbon MM, Roycroft E, Sheehan G, Mc Laughlin AM, Quintyne KI, Brabazon E, O'Meara M, Flanagan PR, Seagar AL, Laurenson IF, Keane J, Rogers TR. False detection of rifampicin resistance using Xpert ® MTB/RIF Ultra assay due to an A451V mutation in Mycobacterium tuberculosis. JAC Antimicrob Resist 2021; 3:dlab101. [PMID: 34386770 PMCID: PMC8355037 DOI: 10.1093/jacamr/dlab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background In a 12 month period, three Irish-born adult cases with pulmonary TB were initially diagnosed by Xpert® MTB/RIF Ultra assay, which detected a rifampicin resistance-conferring mutation prompting treatment as potential MDR cases. Methods Further laboratory investigations on the cultured isolates included GenoType MTBDRplus assay, phenotypic drug susceptibility tests using the BD BACTEC MGIT culture system and MIC broth microdilution tests. Sequencing of the rpoB gene was performed using Sanger sequencing and WGS. Results Phenotypic drug susceptibility tests determined the isolates to be rifampicin susceptible. Molecular investigations identified an A451V (codon 532) mutation in the Mycobacterium tuberculosis rpoB gene that has not previously been found to cause rifampicin resistance. Genome sequencing revealed that the three isolates’ genomes differed by ≤5 SNPs, indicating a high likelihood of recent transmission events. Furthermore, a cluster of six related M. tuberculosis isolates from our in-house typing database showed four were highly related; all were rifampicin susceptible and lacked this mutation. Conclusions False detection of rifampicin resistance, albeit rare, should be considered possible with Xpert® MTB/RIF Ultra assay, particularly in low TB incidence settings. Confirmatory sequencing methods should be performed to prevent the unnecessary use of second-line anti-tuberculous drugs.
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Affiliation(s)
| | - Emma Roycroft
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - Gerard Sheehan
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | | | - Mary O'Meara
- Department of Public Health East, Health Service Executive, Dublin, Ireland
| | - Peter R Flanagan
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - A-Louise Seagar
- Scottish Mycobacteria Reference Laboratory, Edinburgh, Scotland
| | - Ian F Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, Scotland
| | - Joseph Keane
- Department of Respiratory Medicine, St James's Hospital, Dublin, Ireland
| | - Thomas R Rogers
- Irish Mycobacteria Reference Laboratory, St James's Hospital, Dublin, Ireland
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Rudeeaneksin J, Phetsuksiri B, Nakajima C, Bunchoo S, Suthum K, Tipkrua N, Fukushima Y, Suzuki Y. Drug-resistant Mycobacterium tuberculosis and its genotypes isolated from an outbreak in western Thailand. Trans R Soc Trop Med Hyg 2021; 115:886-895. [PMID: 33320938 DOI: 10.1093/trstmh/traa148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/29/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Multidrug-resistant TB (MDR-TB) outbreaks have occurred in the Thamaka district, Kanchanaburi province in Thailand. METHODS Seventy-two isolates, which included 7% mono-, 30.6% MDR and extensively drug-resistant TB (XDR-TB), were genotyped by spoligotyping, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) and single nucleotide polymorphism genotyping, and their drug resistance was analysed. RESULTS The spoligotyping results showed that Beijing spoligo-international type (SIT)1 was predominant (n=38; 52.8%) while the remaining were non-Beijing sublineages (n=34). The MIRU-VNTR analysis showed that Beijing isolates, most of which belonged to the modern type (n=37), formed 5 clusters and 13 individual patterns. In katG, only mutation Ser315Thr was identified. In rpoB, Ser531Leu was predominant, except for His526Arg and Leu533Pro, which were found in two isolates. A cluster of 14 Beijing strains contained these common mutations and shared the MIRU-VNTR genotype with isolates in the Thamaka district that had spread previously. Two U SIT523 isolates contained the mutations A1400G in rrs and Asp94Gly in gyrA genes, indicating a spread of XDR-TB. CONCLUSIONS Most mutations were associated with drug resistance and the specific MDR Beijing and XDR-TB in U SIT523 isolates remain. This genotyping is a key tool for tracking TB transmission in the Thamaka district of Thailand.
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Affiliation(s)
- Janisara Rudeeaneksin
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Benjawan Phetsuksiri
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,International Collaboration Unit, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Supranee Bunchoo
- National Insti tute of Health, Department of Medical Sciences, Nonthaburi Province, Thailand
| | - Krairerk Suthum
- The Office of Disease Prevention and Control 5thRatchaburi, Department of Disease Control, Thailand
| | - Nattakan Tipkrua
- The Office of Disease Prevention and Control 5thRatchaburi, Department of Disease Control, Thailand
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,International Collaboration Unit, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
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91
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Ghielmetti G, Kupca AM, Hanczaruk M, Friedel U, Weinberger H, Revilla-Fernández S, Hofer E, Riehm JM, Stephan R, Glawischnig W. Mycobacterium microti Infections in Free-Ranging Red Deer ( Cervus elaphus). Emerg Infect Dis 2021. [DOI: 10.3201/eid27.210634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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92
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Ghielmetti G, Kupca AM, Hanczaruk M, Friedel U, Weinberger H, Revilla-Fernández S, Hofer E, Riehm JM, Stephan R, Glawischnig W. Mycobacterium microti Infections in Free-Ranging Red Deer (Cervus elaphus). Emerg Infect Dis 2021; 27:2025-2032. [PMID: 34286688 PMCID: PMC8314804 DOI: 10.3201/eid2708.210634] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis–monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.
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93
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Molecular epidemiology and drug susceptibility profiles of Mycobacterium tuberculosis complex isolates from Northern Ghana. Int J Infect Dis 2021; 109:294-303. [PMID: 34273514 DOI: 10.1016/j.ijid.2021.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE We conducted a cross-sectional study in the five administrative regions of Northern Ghana to determine the diversity of Mycobacterium tuberculosis complex (MTBC) sub/lineages and their susceptibility to isoniazid (INH) and rifampicin (RIF). METHODS Sputum specimens were collected and cultured from 566 pulmonary tuberculosis patients reporting to 17 health facilities from 2015 to 2019. Mycobacterial isolates obtained from solid cultures were confirmed as members of the MTBC by PCR amplification of IS6110 and rpoß and assigned lineages and sub-lineages using spoligotyping. RESULTS Of 294 mycobacterial isolates recovered, MTBC species identified were: M. tuberculosis sensu stricto (Mtbss) 241 (82.0%), M. africanum 41 (13.9%) and M. bovis four (1.4%) with eight (2.7%) unidentified. The human-adapted lineages (L) identified (N=279) were L1 (8/279, 2.9%), L2 (15/279, 5.4%), L3 (7/279, 2.5%), L4 (208/279, 74.5%), L5 (13/279, 4.7%) and L6 (28/279, 10.0%) with three unidentified lineages. Among the 208 L4, the dominant sub-lineages in the region were the Cameroon 120/208 (57.7%) and Ghana 50/208 (24.0%). We found 4.4% (13/294) and 0.7% (2/294) of the patients infected with MTBC isolates resistant to INH only and RIF only, respectively, with 2.4% (7/294) being infected with MDR strains. Whereas L6 was associated with the elderly, we identified that the Ghana sub-lineage of L4 was associated with both INH and MDR (p<0.05), making them important TB pathogens in Northern Ghana and a growing public health concern.
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94
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Ordaz-Vázquez A, Torres-González P, Cruz-Hervert P, Ferreyra-Reyes L, Delgado-Sánchez G, García-García L, Kato-Maeda M, Ponce-De-León A, Sifuentes-Osornio J, Bobadilla-Del-Valle M. Genetic diversity and primary drug resistance transmission in Mycobacterium tuberculosis in southern Mexico. INFECTION GENETICS AND EVOLUTION 2021; 93:104994. [PMID: 34245908 DOI: 10.1016/j.meegid.2021.104994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/30/2022]
Abstract
Tuberculosis is a global human health threat, especially in developing countries. The present study aimed to describe the genetic diversity of Mycobacterium tuberculosis and to measure the transmission rates of primary and acquired resistance. A total of 755 M. tuberculosis isolates from a cohort study of patients with culture-confirmed pulmonary tuberculosis in Orizaba, Veracruz, performed between 1995 and 2010 were genotyped by the 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) method. Drug susceptibility was determined. Logistic regression models were constructed to identify the variables associated with resistance and clusters. The recent transmission index (RTI), the Hunter-Gaston discrimination index (HGDI) for the MIRU-VNTR test and allelic diversity (h) were calculated. The Haarlem and LAM lineages were the most common in the population. A total of 519 isolates were grouped into 128 clusters. The overall drug resistance rate was 19%, isoniazid monoresistance (10%) was the most common, and 3.4% of the isolates were multidrug resistant. Among the 116 isolates resistant to at least one drug, the primary and acquired resistance rates were 81.9% and 18.1%, respectively. Primary resistance was associated with belonging to a cluster (aOR 4.05, 95% CI 1.5-11.2, p = 0.007). Previous treatment history (aOR 9.05, 95% CI 3.6-22.5, p < 0.001) and LAM lineage (aOR 4.25, 95% CI 1.4-12.7, p = 0.010) were associated with multidrug-resistant tuberculosis (MDR-TB). The RTI was 51.7%, and the 24-locus MIRU-VNTR HGDI was 0.98. The alleles with the greatest diversity were 4056-QUB26 (h = 0.84), 2163b-QUB11b (h = 0.79), and 424-Mtub04 (h = 0.72). Primary resistance transmission, high LAM lineage prevalence and its association with MDR-TB represent public health problems. The implementation of molecular tools is needed to improve the existing control surveillance tuberculosis program.
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Affiliation(s)
- Anabel Ordaz-Vázquez
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Pedro Torres-González
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Pablo Cruz-Hervert
- Departamento de Salud Pública y Epidemiología Oral, Facultad de Odontología, Universidad Nacional Autonoma de Mexico, Ciudad de México, Mexico
| | - Leticia Ferreyra-Reyes
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Lourdes García-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Midori Kato-Maeda
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alfredo Ponce-De-León
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - José Sifuentes-Osornio
- Departamento de Medicina, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | - Miriam Bobadilla-Del-Valle
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico.
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Zetola NM, Moonan PK, Click E, Oeltmann JE, Basotli J, Wen XJ, Boyd R, Tobias JL, Finlay A, Modongo C. Population-Based Geospatial and Molecular Epidemiologic Study of Tuberculosis Transmission Dynamics, Botswana, 2012-2016. Emerg Infect Dis 2021; 27:835-844. [PMID: 33622470 PMCID: PMC7920683 DOI: 10.3201/eid2703.203840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Tuberculosis (TB) elimination requires interrupting transmission of Mycobacterium tuberculosis. We used a multidisciplinary approach to describe TB transmission in 2 sociodemographically distinct districts in Botswana (Kopanyo Study). During August 2012-March 2016, all patients who had TB were enrolled, their sputum samples were cultured, and M. tuberculosis isolates were genotyped by using 24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats. Of 5,515 TB patients, 4,331 (79%) were enrolled. Annualized TB incidence varied by geography (range 66-1,140 TB patients/100,000 persons). A total of 1,796 patient isolates had valid genotyping results and residential geocoordinates; 780 (41%) patients were involved in a localized TB transmission event. Residence in areas with a high burden of TB, age <24 years, being a current smoker, and unemployment were factors associated with localized transmission events. Patients with known HIV-positive status had lower odds of being involved in localized transmission.
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96
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Oudghiri A, Momen G, Aainouss A, Laglaoui A, El Messaoudi MD, El Mzibri M, Chaoui I. Genotypic diversity of multi- and pre-extremely drug-resistant Mycobacterium tuberculosis isolates from Morocco. PLoS One 2021; 16:e0253826. [PMID: 34214120 PMCID: PMC8253442 DOI: 10.1371/journal.pone.0253826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/13/2021] [Indexed: 12/02/2022] Open
Abstract
In Morocco, the prevalence of multidrug resistant tuberculosis (MDR-TB) continues to increase especially within previously treated cases; these MDR cases may evolve to extensively drug resistant tuberculosis (XDR-TB) raising major concern to TB control programs. From an epidemiological window, scarce informations are available about the genetic diversity of Mycobacterium tuberculosis (MTB) strains fueling these forms of resistance. The aim of this study was to assess to genetic diversity of MDR-MTB strains. Hence, this prospective study was conducted on patients diagnosed with MDR-TB at Pasteur Institute of Casablanca from 2010 to 2013. A total of 70 MDR-MTB isolates were genotyped by spoligotyping and 15-loci MIRU-VNTR methods. Spoligotyping generated four orphan patterns, five unique profiles whereas 61 strains were grouped in nine clusters (2 to 25 strains per cluster), the clustering rates being 87.1%. Subtyping by 15 loci MIRU-VNTR splitted all clusters already established by spoligotyping and generated 70 unique profiles not recognized in SITVIT2 database; clustering rate was equal to zero. HGDI analysis of 15 loci MIRU demonstrated that eight out of 15 loci were highly discriminant. Of note, all pre-XDR strains belongs to many clades, meaning that there no association between gyrA mutants and particular clade. Overall, the data generated by this study (i) describe the population structure of MDR MTBC in Morocco which is highly homogenous, (ii) confirm that TB in Morocco is almost exclusively transmitted by modern and evolutionary lineages with high level of biodiversity seen by MIRU, and (iii) validate the use of optimized 15-loci MIRU-VNTR format for future investigations in Morocco.
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Affiliation(s)
- Amal Oudghiri
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
- Faculty of Sciences and Techniques, Biotechnology and Bimolecular Engineering Research Laboratory, Tangier, Morocco
| | - Ghizlane Momen
- Laboratory of Mycabacteria, Pasteur Institute of Morocco, Casablanca, Morocco
- Faculty of Sciences, Laboratory of Microbiology Pharmacology, Biotechnology and Environment, Casablanca, Morocco
| | - Achraf Aainouss
- Laboratory of Mycabacteria, Pasteur Institute of Morocco, Casablanca, Morocco
- Faculty of Sciences Ben M’Sik, Laboratory of Ecology and Environment, Casablanca, Morocco
| | - Amin Laglaoui
- Faculty of Sciences and Techniques, Biotechnology and Bimolecular Engineering Research Laboratory, Tangier, Morocco
| | | | - Mohammed El Mzibri
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
| | - Imane Chaoui
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
- * E-mail: ,
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Tafess K, Beyen TK, Girma S, Girma A, Siu G. Spatial clustering and genetic diversity of Mycobacterium tuberculosis isolate among pulmonary tuberculosis suspected patients, Arsi Zone, Ethiopia. BMC Pulm Med 2021; 21:206. [PMID: 34193091 PMCID: PMC8244181 DOI: 10.1186/s12890-021-01567-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tuberculosis remains a serious public health concern globally. The enormous social, economic, and health impacts of the diseases are attributed to the lack of updated data on the prevalence, geospatial distribution, population structures, and genotypic variants of the circulating M. tuberculosis. METHODS Structured questionnaire, mycobacterial culture, and standard 24-Mycobacterial Interspersed Repeated Units-Variable Number Tandem Repeats (MIRU-VNTR) were employed to collect sociodemographic characters, residence linked information, and genotype the isolates. The retrospective discrete Bernoulli model was used to identify the hot spot districts of sputum smear positivity, and Web-based Miru-VNTRPlus were used for the identification of lineages and sublineages. RESULTS Out of 832 presumptive pulmonary tuberculosis (PTB) suspects, 119 (14.3%) were smear-positive. In the multivariate binary logistic model, PTB suspected patients in the age groups of 7-25 and 25-34 and those from rural residents were 4.53 (AOR = 4.53; 95% CI 2.25-9.13), 3.00 (AOR = 3.00; 95% CI 1.41-6.35) and 1.65 (AOR = 1.65; 95% CI 1.01-2.70) times at higher risk of turning smear-positive. Eleven (47.8%) districts of Arsi Zone were shown to have a high rate of clustering (RR = 2.27; 95% CI 1.62-3.2) of smear-positive PTB. Of 72 isolates queried for the lineage assignment, 59 (81.9%) were classified into the previously known lineages and 13 (18.1%) were not assigned to any known lineages. Overall, 42 (58.3%) belong to M. tuberculosis lineage 4 (Euro-American), 16 (22.2%) M. tuberculosis lineage 3 (Delhi/CAS), and 1 (1.4%) M. tuberculosis Lineage 1 (Indo-Oceanic/ East Africa Indian). Further classification to the sublineage indicates that the predominant lineage was Delhi/CAS comprising 16 (22.2%) isolates followed by 15 (20.8%) isolates belonging to Haarlem. The remaining isolates were distributed as 13 (18.1%) TUR, 6 (8.3%) LAM, 4 (5.5%) URAL, 4 (4.5%) NEW-1 and 1 (1.4%) EAI. CONCLUSION Our study showed higher smear-positive results among PTB suspected patients and remarkable spatial variation across districts of Arsi Zone in smear-positive PTB. This information together with the genotypic features could be used as input for the efforts of designing control strategies.
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Affiliation(s)
- Ketema Tafess
- Institute of Pharmaceutical Science, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Teresa Kisi Beyen
- Department of Public Health, College of Health Sciences, Arsi University, Asella, Ethiopia
| | - Sisay Girma
- Department of Clinical Study, College of Veterinary Medicine and Agriculture, Addis Ababa University, P. O. Box 34, Bishoftu, Ethiopia
| | - Asnakech Girma
- Disease Prevention, Training and Research Division, Federal Prison General Hospital, Addis Ababa, Ethiopia
| | - Gilman Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
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Moonan PK, Zetola NM, Tobias JL, Basotli J, Boyd R, Click ES, Dima M, Fane O, Finlay AM, Ogopotse M, Wen XJ, Modongo C, Oeltmann JE. A Neighbor-Based Approach to Identify Tuberculosis Exposure, the Kopanyo Study. Emerg Infect Dis 2021; 26:1010-1013. [PMID: 32310058 PMCID: PMC7181937 DOI: 10.3201/eid2605.191568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Contact investigation is one public health measure used to prevent tuberculosis by identifying and treating persons exposed to Mycobacterium tuberculosis. Contact investigations are a major tenet of global tuberculosis elimination efforts, but for many reasons remain ineffective. We describe a novel neighbor-based approach to reframe contact investigations.
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99
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Baik Y, Modongo C, Moonan PK, Click ES, Tobias JL, Boyd R, Finlay A, Oeltmann JE, Shin SS, Zetola NM. Possible Transmission Mechanisms of Mixed Mycobacterium tuberculosis Infection in High HIV Prevalence Country, Botswana. Emerg Infect Dis 2021; 26:953-960. [PMID: 32310078 PMCID: PMC7181944 DOI: 10.3201/eid2605.191638] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis caused by concurrent infection with multiple Mycobacteriumtuberculosis strains (i.e., mixed infection) challenges clinical and epidemiologic paradigms. We explored possible transmission mechanisms of mixed infection in a population-based, molecular epidemiology study in Botswana during 2012–2016. We defined mixed infection as multiple repeats of alleles at >2 loci within a discrete mycobacterial interspersed repetitive unit–variable-number tandem-repeat (MIRU-VNTR) result. We compared mixed infection MIRU-VNTR results with all study MIRU-VNTR results by considering all permutations at each multiple allele locus; matched MIRU-VNTR results were considered evidence of recently acquired strains and nonmatched to any other results were considered evidence of remotely acquired strains. Among 2,051 patients, 34 (1.7%) had mixed infection, of which 23 (68%) had recently and remotely acquired strains. This finding might support the mixed infection mechanism of recent transmission and simultaneous remote reactivation. Further exploration is needed to determine proportions of transmission mechanisms in settings where mixed infections are prevalent.
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100
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Rodríguez-Grande C, Hurtado JC, Rodríguez-Maus S, Casas I, Castillo P, Navarro M, Rakislova N, García-Basteiro A, Carrilho C, Fernandes F, Lovane L, Jordao D, Ismail MR, Lorenzoni C, Cossa A, Mandomando I, Bassat Q, Menéndez C, Ordi J, Muñoz P, Pérez-Lago L, García de Viedma D, Martínez MJ. High within-host diversity found from direct genotyping on post-mortem tuberculosis specimens in a high-burden setting. Clin Microbiol Infect 2021; 27:1518.e5-1518.e9. [PMID: 34119641 DOI: 10.1016/j.cmi.2021.05.038] [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: 03/16/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To characterize the clonal complexity in Mycobacterium tuberculosis (MTB) infections considering factors that help maximize the detection of coexisting strains/variants. METHODS Genotypic analysis by Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeats (MIRU-VNTR) was performed directly on 70 biopsy specimens from two or more different tissues involving 28 tuberculosis cases diagnosed post-mortem in Mozambique, a country with a high tuberculosis burden. RESULTS Genotypic data from isolates collected from two or more tissues were obtained for 23 of the 28 cases (82.1%), allowing the analysis of within-patient diversity. MIRU-VNTR analysis revealed clonal diversity in ten cases (35.7%). Five cases showed allelic differences in three or more loci, suggesting mixed infection with two different strains. In half of the cases showing within-host diversity, one of the specimens associated with clonal heterogeneity was brain tissue. CONCLUSIONS Direct MTB genotyping from post-mortem tissue samples revealed a frequent within-host Mycobacterium tuberculosis diversity, including mixed and polyclonal infections. Most of this diversity would have been overlooked if only standard analysis of respiratory specimens had been performed.
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Affiliation(s)
- Cristina Rodríguez-Grande
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Juan Carlos Hurtado
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Microbiology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Sandra Rodríguez-Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Isaac Casas
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Microbiology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Paola Castillo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Mireia Navarro
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Microbiology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Natalia Rakislova
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Alberto García-Basteiro
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Carla Carrilho
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Fabiola Fernandes
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Lucilia Lovane
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Dercio Jordao
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Mamudo R Ismail
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Cesaltina Lorenzoni
- Department of Pathology, Maputo Central Hospital, Maputo, Mozambique; Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Anélsio Cossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ICREA, Catalan Institution for Research and Advanced Studies, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Paediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Clara Menéndez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Jaume Ordi
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain; Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain.
| | - Miguel J Martínez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Department of Microbiology, Hospital Clinic de Barcelona, Barcelona, Spain.
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