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Borji S, Kooti S, Ramazanzadeh R, Kadivarian S, Atashi S, Mohajeri P. Antimicrobial resistance profile and prevalence of Mycobacterium tuberculosis complex in Western Iran using spoligotyping method. J Clin Tuberc Other Mycobact Dis 2024; 36:100467. [PMID: 39184015 PMCID: PMC11342116 DOI: 10.1016/j.jctube.2024.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease with multiple manifestations and gradual progression that remains a major health problem and a leading cause of death worldwide. In recent years, a number of DNA fingerprinting techniques have been developed to identify strains of the Mycobacterium tuberculosis (MTB) complex. Spoligotyping is one of the first PCR-based genotyping methods. Information on the number and identification of common strains among MTB complex samples in clinical samples from Kermanshah city is needed to develop more effective therapeutic strategies. This is a descriptive cross-sectional study of 41 sample patients with TB referred to Kermanshah Tuberculosis Centre between December 2021 and June 2022, including sputum, aspiration, urine, etc. First, the susceptibility of the developed bacteria to culture media was compared with that of isoniazid using the proportional method, and rifampin was determined according to the standard protocol. Demographic data of patients referred to the Centre for the Control of Lung Diseases were also recorded. In the next step, spoligotyping was carried out using the standard method and each strain pattern was recorded as an OCTAL code and compared with the information available at the World Bank on spoligotyping and its strains. Forty-one patients with pulmonary TB were tested using spoligotyping. Four MTB strains were identified, including H4, CAS, T1 and H1. The H4 strain also had the highest frequency with 16 samples (39%) among the MTB complex strains isolated using spoligotyping. The highest frequency of strains isolated using spoligotyping was associated with the H4 strain. It can be concluded that spoligotyping is very cost effective, simple, repeatable and highly sensitive.
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Affiliation(s)
- Soroush Borji
- Student Research Committee, Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Kooti
- Environment Technologies Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rashid Ramazanzadeh
- Department of Microbiology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sepide Kadivarian
- Student Research Committee, Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Atashi
- West Tuberculosis Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parviz Mohajeri
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Research Institute for Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Dekhil N, Mardassi H. Delineating the evolutionary pathway to multidrug-resistant outbreaks of a Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage. Int J Infect Dis 2024; 144:107077. [PMID: 38697608 DOI: 10.1016/j.ijid.2024.107077] [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: 02/20/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES We sought to capture the evolutionary itinerary of the Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, where it caused a major multidrug-resistant (MDR) tuberculosis outbreak in a context strictly negative for HIV infection. METHODS We combined whole genome sequencing and Bayesian approaches using a representative collection of drug-susceptible and drug-resistant L4.1.2.1/Haarlem clinical strains (n = 121) recovered from the outbreak region over 16 years. RESULTS In the absence of drug resistance, the L4.1.2.1/Haarlem sublineage showed a propensity for rapid transmission as witnessed by the high clustering (44.6%) and recent transmission rates (25%), as well as the reduced mean distance between genome pairs. The entire pool of L4.1.2.1/Haarlem MDR strains was found to be linked to either the aforementioned major outbreak (68 individuals, 2001-2016) or to a minor, newly uncovered outbreak (six cases, 2001-2011). Strikingly, the two outbreaks descended independently from a common ancestor that can be dated back to 1886. CONCLUSIONS Our data point to the intrinsic propensity for rapid transmission of the M. tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, linking the overall MDR tuberculosis epidemic to a single ancestor. These findings bring out the important role of the bacillus' genetic background in the emergence of successful MDR M. tuberculosis clones.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
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Bouzouita I, Draoui H, Cabibbe AM, Essalah L, Bejaoui S, Trovato A, Messadi F, Cirillo DM, Slim-Saidi L. Performance of the GenoType MTBDRsl V 2.0 for detecting second-line drugs resistance of Mycobacterium tuberculosis isolates in Tunisia. Res Microbiol 2021; 172:103816. [PMID: 33737037 DOI: 10.1016/j.resmic.2021.103816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/06/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Rapid detection of the second-line drug (SLD) resistant tuberculosis (TB) strains is challenging to prescribe an immediate adequate treatment and limit the transmission of SLD resistant strains. The study aimed to evaluate the performance of GenoType MTBDRsl V2.0 compared to phenotypic drug susceptibility testing (pDST:MGIT960) to detect resistance to SLD of Mycobacterium tuberculosis (MTB) isolates in Tunisia, between May 2015 and December 2019. As a matter of fact, 103 rifampicin-resistant and multidrug-resistant MTB strains were included. Discrepancies between pDST and MTBDRsl were solved by whole genome sequencing. Compared to pDST, MTBDRsl V2.0 showed a sensitivity of 92.8% (68.5%-98.7%) in detecting resistance to fluoroquinolones. As for second-line injectable drugs, it presented a sensitivity of 80.0% (49.0%-94.3%). MTBDRsl had sensitivities of 100.0% (67.5%-100.0%), 75.0% (40.9%-92.8%) and 100.0% (60.9%-100.0%) respectively for kanamycin, capreomycin and amikacin. The specificity was 100.0% for all the drugs evaluated. As for diagnosing XDR-TB, it had a sensitivity of 57.1% (25.0%-84.1%) and a specificity of 100.0% (96.1%-100.0%). MTBDRsl V2.0 showed a high performance in detecting SLD resistance with a short turnaround time compared with pDST, which made it possible to start an early treatment and to maintain a low prevalence of SLD resistance and XDR-TB in Tunisia.
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Affiliation(s)
- Imen Bouzouita
- National Reference Laboratory for Mycobacteria, A. Mami Pneumology Hospital, Ariana, Tunisia; University of Tunis El Manar, Faculty of Mathematical, Physical and Natural Sciences of Tunis, Tunis, Tunisia.
| | - Henda Draoui
- National Reference Laboratory for Mycobacteria, A. Mami Pneumology Hospital, Ariana, Tunisia.
| | - Andrea Maurizio Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy.
| | - Leila Essalah
- National Reference Laboratory for Mycobacteria, A. Mami Pneumology Hospital, Ariana, Tunisia.
| | - Sana Bejaoui
- National Reference Laboratory for Mycobacteria, A. Mami Pneumology Hospital, Ariana, Tunisia.
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy.
| | - Férièle Messadi
- Bacteriology Laboratory, Hedi Chaker Hospital, Sfax, Tunisia.
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy.
| | - Leila Slim-Saidi
- National Reference Laboratory for Mycobacteria, A. Mami Pneumology Hospital, Ariana, Tunisia.
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Skhairia MA, Dekhil N, Mhenni B, Fradj SB, Mardassi H. Successful expansion of Mycobacterium tuberculosis Latin American and Mediterranean sublineage (L4.3/LAM) in Tunisia mainly driven by a single, long-established clonal complex. Int J Infect Dis 2020; 103:220-225. [PMID: 33307222 DOI: 10.1016/j.ijid.2020.11.195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To explore the evolutionary history of Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in Tunisia, where it predominates. METHODS High-resolution genotyping of 252 L4.3/LAM clinical strains was undertaken, and whole-genome sequencing was performed on 31 representative isolates. RESULTS Genotyping data coupled with Bayesian analyses split the Tunisian L4.3/LAM strain collection into two divergent entities (65.07% vs 34.92%): a major subpopulation, dominated by a single clonal complex (CC), TUN4.3_CC1 (94.51%); and a minor subpopulation, dominated by TUN4.3_CC2 (42.04%). TUN4.3_CC1 is clearly thriving in Tunisia, accounting for 61.5% of the L4.3/LAM sublineage. TUN4.3_CC1 displayed higher mean allelic richness compared with TUN4.3_CC2 and predominated throughout the entire region, indicating a long-established history. The very low proportion of drug resistance among TUN4.3_CC1 isolates is indicative of their intrinsic ability to spread successfully in the host population. Genomic analyses further confirmed the clear genetic separation between the two main CCs (pairwise fixation index 0.56), and suggested the relatively ancient origin of TUN4.3_CC1. Consistent with its successful expansion, TUN4.3_CC1 showed reduced mean pairwise genetic distance between genomes. CONCLUSIONS These findings link the successful expansion of L4.3/LAM in Tunisia to a single long-established clone.
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Affiliation(s)
- Mohamed Amine Skhairia
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Naira Dekhil
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Saloua Ben Fradj
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
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Chisompola NK, Streicher EM, Muchemwa CMK, Warren RM, Sampson SL. Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review. BMC Infect Dis 2020; 20:344. [PMID: 32404119 PMCID: PMC7222473 DOI: 10.1186/s12879-020-05031-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Background The burden of drug resistant tuberculosis in Africa is largely driven by the emergence and spread of multidrug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis strains. MDR-TB is defined as resistance to isoniazid and rifampicin, while XDR-TB is defined as MDR-TB with added resistance to any of the second line injectable drugs and any fluoroquinolone. The highest burden of drug resistant TB is seen in countries further experiencing an HIV epidemic. The molecular mechanisms of drug resistance as well as the evolution of drug resistant TB strains have been widely studied using various genotyping tools. The study aimed to analyse the drug resistant lineages in circulation and transmission dynamics of these lineages in Africa by describing outbreaks, nosocomial transmission and migration. Viewed as a whole, this can give a better insight into the transmission dynamics of drug resistant TB in Africa. Methods A systematic review was performed on peer reviewed original research extracted from PubMed reporting on the lineages associated with drug resistant TB from African countries, and their association with outbreaks, nosocomial transmission and migration. The search terms “Tuberculosis AND drug resistance AND Africa AND (spoligotyping OR molecular epidemiology OR IS6110 OR MIRU OR DNA fingerprinting OR RFLP OR VNTR OR WGS)” were used to identify relevant articles reporting the molecular epidemiology of drug resistant TB in Africa. Results Diverse genotypes are associated with drug resistant TB in Africa, with variations in strain predominance within the continent. Lineage 4 predominates across Africa demonstrating the ability of “modern strains” to adapt and spread easily. Most studies under review reported primary drug resistance as the predominant type of transmission. Drug resistant TB strains are associated with community and nosocomial outbreaks involving MDR- and XDR-TB strains. The under-use of molecular epidemiological tools is of concern, resulting in gaps in knowledge of the transmission dynamics of drug resistant TB on the continent. Conclusions Genetic diversity of M. tuberculosis strains has been demonstrated across Africa implying that diverse genotypes are driving the epidemiology of drug resistant TB across the continent.
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Affiliation(s)
- Namaunga Kasumu Chisompola
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. .,Department of Basic Medical Sciences, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola, Zambia.
| | - Elizabeth Maria Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | - Robin Mark Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha Leigh Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Tafaj S, Mokrousov I, Borroni E, Trovato A, Kapisyzi P, Bardhi D, Hafizi H, Bala S, Bulo A, Bino S, Rastogi N, Cirillo D. Peculiar features of the Mycobacterium tuberculosis population structure in Albania. INFECTION GENETICS AND EVOLUTION 2019; 78:104136. [PMID: 31830600 DOI: 10.1016/j.meegid.2019.104136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/21/2022]
Abstract
Albania is a Balkan country with moderate to low incidence of tuberculosis (TB) and very low prevalence of drug resistant TB. Here, we analyzed a country-wide multi-year Mycobacterium tuberculosis collection in order to detect possible dynamic trends of TB in Albania, with a focus on drug resistance and endemic/epidemic clones. In total, 743 isolates collected in 2007 to 2011 were divided into 107 spoligotypes and 351 MIRU-types. Based on the MIRU-VNTR phylogenetic analysis, the isolates were assigned to the following lineages/families: animal ecotypes (5 M. bovis and 2 M. caprae isolates), Lineage 2 (5 Beijing isolates), Lineage 3 (1 CAS-Delhi isolate) and, mostly and overwhelmingly, Lineage 4 (Cameroon, Uganda, Ghana and related; NEW-1-related; Ural, Haarlem, LAM, S, TUR; and unclassified isolates). Most of the isolates (452/743) were intermediately located on the global VNTR tree and did not cluster with any reference profile; they were distantly related to different families within Lineage 4 and we designated them as "unclassified L4" isolates. The significantly higher proportion of drug resistance was observed in (i) Beijing genotype compared to all other isolates (60%, P = .008), (ii) "unclassified L4" compared to all other isolates (13.9%, P = .04) and (iii) SIT2936 compared to other "unclassified L4" (34.3%, P = .0006). Analysis of the yearly collections revealed (i) some decrease of the large heterogeneous "unclassified L4" from 65% to 57%; (ii) steadily increasing gradient of LAM from 3.4 to 13.3%; (iii) stable prevalence of Haarlem (15-20%); and (iv) decrease of TUR with only 1.1% in 2011. Most of the LAM (33/49) and Beijing (3/5) isolates belonged to the VNTR types specific for Russia and former Soviet Union countries. To conclude, our results highlight a peculiar nature of M. tuberculosis population in Albania that is dominated by local and unclassified genotypes within Lineage 4, and also features European genotypes and epidemically relevant clones originating from the former Soviet Union countries. At the same time, these imported clones remain drug susceptible and prevalence of drug resistance on a whole is low.
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Affiliation(s)
- Silva Tafaj
- National TB Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania.
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, Division of Immunology and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, Division of Immunology and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Perlat Kapisyzi
- National TB Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Donika Bardhi
- National TB Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Hasan Hafizi
- National TB Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Silvana Bala
- National TB Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Anyla Bulo
- Laboratory Department, University of Medicine, Tirana, Albania
| | - Silvia Bino
- Control of Infectious Diseases Department, Institute of Public Health, Tirana, Albania
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Daniela Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Bhembe NL, Nwodo UU, Okoh AI, Obi CL, Mabinya LV, Green E. Clonality and genetic profiles of drug-resistant Mycobacterium tuberculosis in the Eastern Cape Province, South Africa. Microbiologyopen 2019; 8:e00449. [PMID: 30801981 PMCID: PMC6436438 DOI: 10.1002/mbo3.449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 01/05/2023] Open
Abstract
In this study, we investigated the diversity of drug-resistant Mycobacterium tuberculosis isolates from families who own cattle in the Eastern Cape Province of South Africa using spoligotyping and mycobacterial interspersed repetitive-unit-variable number tandem repeat (MIRU-VNTR) typing. The Mycobacterium tuberculosis was investigated using MIRU-VNTR and the Mycobacterium tuberculosis families were evaluated using spoligotyping. Spoligotyping grouped 91% of the isolates into seven clusters, while 9% of the deoxyribonucleic acid (DNA) from TB isolates were unclustered from a total of 154 DNA used. Previously described shared types were observed in 89.6% of the isolates, with the Beijing family, SIT1, the principal genotype in the province, while the families T, SIT53 and X1, SIT1329 were the least detected genotypes. MIRU-VNTR grouped 81% of the isolates in 23 clusters while 19% were unclustered. A combination of the VNTR and spoligotyping grouped 79% of the isolates into 23 clusters with 21% unclustered. The low level of diversity and the clonal spread of drug-resistant Mycobacterium tuberculosis isolates advocate that the spread of TB in this study may be instigated by the clonal spread of Beijing genotype. The results from this study provide vital information about the lack of TB control and distribution of Mycobacterium tuberculosis complex strain types in the Eastern Cape Province of South Africa.
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Affiliation(s)
- Nolwazi L Bhembe
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Chikwelu L Obi
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Academic and Research Division, University of Fort Hare, Alice, South Africa
| | - Leonard V Mabinya
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Molecular Pathogenesis and Molecular Epidemiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Ezekiel Green
- Department of Biotechnology and Food Science, Faculty of Science, University of Johannesburg, Doornfontein, South Africa
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Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3683801. [PMID: 29850506 PMCID: PMC5914149 DOI: 10.1155/2018/3683801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/10/2018] [Indexed: 02/04/2023]
Abstract
Tuberculosis (TB) remains a major health challenge in South Africa and the condition in humans has been well researched and documented. However, investigations on the circulating Mycobacterium tuberculosis complex (MTBC) strains from cattle in the Eastern Cape Province of South Africa are insufficient. This study delineated the diversity of MTBC isolates from cows' lymph nodes. A total of 162 MTBC isolates, collected over a one-year period from cattle lymph nodes from two abattoirs, were submitted to spoligotyping and 12 MIRU-VNTR typing. The spoligotyping results were matched with isolates in the universal spoligotyping database (SITVIT2). Our study identified 27 spoligotype patterns, with 10 shared types assigned to five lineages: the East-Asian (Beijing) was predominant, 17.9%, and East-Asian (Microti) and Latin-American-Mediterranean S were the least detected with 0.6%. Spoligotyping showed a higher clustering rate of 82.1%, with the lowest being the Hunter-Gaston Diversity Index (HGDI) of 0.485; 12 MIRU-VNTR resulted in a clustering rate of 64.8%, showing a higher HGDI of 0.671. The results of this study show a high diversity of MTBC strains in the Eastern Cape Province and clustering rate, which indicates ongoing transmission in the province.
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Dekhil N, Meftahi N, Mhenni B, Ben Fraj S, Haltiti R, Belhaj S, Mardassi H. MDR-TB Outbreak among HIV-Negative Tunisian Patients followed during 11 Years. PLoS One 2016; 11:e0153983. [PMID: 27124599 PMCID: PMC4849785 DOI: 10.1371/journal.pone.0153983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/06/2016] [Indexed: 01/09/2023] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) outbreaks that evolve, from the outset, in a context strictly negative for HIV infection deserve special consideration since they reflect the true intrinsic epidemic potential of the causative strain. To our knowledge, the long-term evolution of such exceptional outbreaks and the treatment outcomes for the involved patients has never been reported hitherto. Here we provide a thorough description, over an 11-year period, of an MDR-TB outbreak that emerged and expanded in an HIV-negative context, Northern Tunisia. Methodology/Principal Findings From October 2001 to June 2011, the MDR-TB outbreak involved 48 HIV-negative individuals that are mainly young (mean age 31.09 yrs; 89.6% male) and noninstitutionalized. Drug susceptibility testing coupled to mutational analysis revealed that initial transmission involved an isolate that was simultaneously resistant to isoniazid, rifampicin, ethambutol, and streptomycin. The causative Haarlem3-ST50 outbreak strain expanded mainly as an 11-banded IS6110 RFLP profile (77.1%), from which a 12-banded subclone evolved. After undergoing a 2-year treatment with second-line drugs, 22 (45.8%) patients were cured and 3 (6.2%) completed treatment, thus yielding an overall treatment success rate of 52.1%. Among the patients that experienced unfavorable treatment outcomes, 10 (20.8%) failed treatment, 3 (6.2%) were lost to follow-up, 5 (10.4%) died, and 5 (10.4%) could not be evaluated. Poor adherence to treatment was found to be the main independent predictor of unfavorable outcomes (HR: 9.15; 95% CI 1.72–48.73; P = 0.014). Intriguingly, the evolved 12-banded subclone proved significantly associated with unfavorable outcomes (HR: 4.90; 95% CI 1.04–23.04, P = 0.044). High rate of fatality and relapse was further demonstrated at the long-term, since 70% of those whose treatment failed have died, and 24% among those deemed successfully treated have relapsed. Conclusions/Significance Taken together, the data obtained in this study indicate that MDR-TB clinical isolates could become fit enough to cause large and severe outbreaks in an HIV-negative context. Such MDR-TB outbreaks are characterized by low treatment success rates and could evolve towards increased severity, thus calling for early detection of cases and the necessity to raise the bar of surveillance throughout and beyond the treatment period.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Nedra Meftahi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Saloua Ben Fraj
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Raja Haltiti
- Hôpital Régional de Menzel-Bourguiba, Menzel Bourguiba, Tunisia
| | - Sameh Belhaj
- Hôpital Régional de Menzel-Bourguiba, Menzel Bourguiba, Tunisia
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- * E-mail:
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Mokrousov I, Vyazovaya A, Iwamoto T, Skiba Y, Pole I, Zhdanova S, Arikawa K, Sinkov V, Umpeleva T, Valcheva V, Alvarez Figueroa M, Ranka R, Jansone I, Ogarkov O, Zhuravlev V, Narvskaya O. Latin-American-Mediterranean lineage of Mycobacterium tuberculosis: Human traces across pathogen's phylogeography. Mol Phylogenet Evol 2016; 99:133-143. [PMID: 27001605 DOI: 10.1016/j.ympev.2016.03.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/10/2016] [Accepted: 03/15/2016] [Indexed: 01/18/2023]
Abstract
Currently, Mycobacterium tuberculosis isolates of Latin-American Mediterranean (LAM) family may be detected far beyond the geographic areas that coined its name 15years ago. Here, we established the framework phylogeny of this geographically intriguing and pathobiologically important mycobacterial lineage and hypothesized how human demographics and migration influenced its phylogeography. Phylogenetic analysis of LAM isolates from all continents based on 24 variable number of tandem repeats (VNTR) loci and other markers identified three global sublineages with certain geographic affinities and defined by large deletions RD115, RD174, and by spoligotype SIT33. One minor sublineage (spoligotype SIT388) appears endemic in Japan. One-locus VNTR signatures were established for sublineages and served for their search in published literature and geographic mapping. We suggest that the LAM family originated in the Western Mediterranean region. The most widespread RD115 sublineage seems the most ancient and encompasses genetically and geographically distant branches, including extremely drug resistant KZN in South Africa and LAM-RUS recently widespread across Northern Eurasia. The RD174 sublineage likely started its active spread in Brazil; its earlier branch is relatively dominated by isolates from South America and the derived one is dominated by Portuguese and South/Southeastern African isolates. The relatively most recent SIT33-sublineage is marked with enigmatic gaps and peaks across the Americas and includes South African clade F11/RD761, which likely emerged within the SIT33 subpopulation after its arrival to Africa. In addition to SIT388-sublineage, other deeply rooted, endemic LAM sublineages may exist that remain to be discovered. As a general conclusion, human mass migration appears to be the major factor that shaped the M. tuberculosis phylogeography over large time-spans.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia.
| | - Anna Vyazovaya
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia
| | - Tomotada Iwamoto
- Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku, Kobe 650-0046, Japan
| | - Yuriy Skiba
- Aitkhozhin Institute of Molecular Biology and Biochemistry, 86, Dosmuhamedov str., Almaty 050012, Kazakhstan
| | - Ilva Pole
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, Riga LV-1067, Latvia; Center of Tuberculosis and Lung Diseases, Riga East University Hospital, Stopinu p., Riga LV-2118, Latvia
| | - Svetlana Zhdanova
- Scientific Center of Family Health and Reproductive Problems, Irkutsk 664003, Russia
| | - Kentaro Arikawa
- Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku, Kobe 650-0046, Japan
| | - Viacheslav Sinkov
- Scientific Center of Family Health and Reproductive Problems, Irkutsk 664003, Russia
| | - Tatiana Umpeleva
- Ural Research Institute of Phthisiopulmonology, 50 22go Partsiezda str., Ekaterinburg 620039, Russia
| | - Violeta Valcheva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26 Acad. G Bonchev str., Sofia 1113, Bulgaria
| | - Maria Alvarez Figueroa
- Central Research Institute for Epidemiology, 3A Novogireevskaya str., Moscow 111123, Russia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, Riga LV-1067, Latvia
| | - Inta Jansone
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, Riga LV-1067, Latvia
| | - Oleg Ogarkov
- Scientific Center of Family Health and Reproductive Problems, Irkutsk 664003, Russia
| | - Viacheslav Zhuravlev
- Research Institute of Phthisiopulmonology, 2-4 Ligovsky prospect, St. Petersburg 191036, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia; Research Institute of Phthisiopulmonology, 2-4 Ligovsky prospect, St. Petersburg 191036, Russia
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11
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Diab HM, Nakajima C, Kotb SA, Mokhtar A, Khder NFM, Abdelaal ASA, Hegazy A, Poudel A, Shah Y, Suzuki Y. First insight into the genetic population structure of Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in Egypt. Tuberculosis (Edinb) 2015; 96:13-20. [PMID: 26786649 DOI: 10.1016/j.tube.2015.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/31/2015] [Accepted: 11/08/2015] [Indexed: 11/19/2022]
Abstract
The present study aimed to assess the population structure of Mycobacterium tuberculosis (MTB) isolates from Egypt. A total of 230 MTB isolates were analysed using spoligotyping, large sequence polymorphism (LSPs), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and multi-locus sequence typing (MLST). The majority of isolates (93.0%) belonged to lineage 4, including 44.3, 13.4 and 10.8% of the ill-defined T clade, LAM and Haarlem families, respectively, and lineage 3 was identified in 7.0% of the isolates. MIRU-VNTRs typing allowed efficient discrimination of the spoligotype-defined clusters, including spoligo-international types (SIT) 53, 34, and 4, into 56 patterns, including 13 clusters and 43 unique patterns. A new SNP at position 311614 was identified in all six isolates to form the biggest MIRU-VNTR cluster, which suggested a recent clonal expansion. This SNP could possibly be used as a genetic marker for robust discriminations of Egyptian MTB isolates belonging to SIT53. The combination of spoligotyping, 12 MIRU-VNTRs loci and MLST provided insight into the genetic diversity and transmission dynamics of the Egyptian MTB genotypes and could be a key to implementation of effective control measures by public health authorities.
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Affiliation(s)
- Hassan Mahmoud Diab
- Department of Animal Hygiene, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan
| | - Saber A Kotb
- Department of Animal Hygiene, Faculty of Veterinary Medicine, Assiut University, Egypt
| | - Alaa Mokhtar
- National Tuberculosis Control Program, Ministry of Health and Population, Egypt
| | - Nagwa F M Khder
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ahmed S A Abdelaal
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Azza Hegazy
- TB Supranational Reference Laboratory, Central Public Health Laboratories, Clinical Microbiology Department, Ministry of Health and Population, Egypt
| | - Ajay Poudel
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yogendra Shah
- 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; Hokkaido University, The Global Station for Zoonosis Control, Sapporo, Japan.
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12
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Meftahi N, Namouchi A, Mhenni B, Brandis G, Hughes D, Mardassi H. Evidence for the critical role of a secondary site rpoB mutation in the compensatory evolution and successful transmission of an MDR tuberculosis outbreak strain. J Antimicrob Chemother 2015; 71:324-32. [PMID: 26538504 DOI: 10.1093/jac/dkv345] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/24/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND MDR Mycobacterium tuberculosis clinical strains that cause large outbreaks, particularly among HIV-negative patients, are likely to have undergone the most successful compensatory evolution. Hence, mutations secondary to the acquisition of drug resistance are worthy of consideration in these highly transmissible strains. Here, we assessed the role of a mutation within rpoB, rpoB V615M, secondary to the rifampicin resistance-conferring mutation rpoB S531L, which is associated with a major MDR tuberculosis outbreak strain that evolved in an HIV-negative context in northern Tunisia. METHODS Using BCG as a model organism, we engineered strains harbouring either the rpoB S531L mutation alone or the double mutation rpoB S531L, V615M. Individual and competitive in vitro growth assays were performed in order to assess the relative fitness of each BCG mutant. RESULTS The rpoB V615M mutation was found to be invariably associated with rpoB S531L. Structural analysis mapped rpoB V615M to the same bridge helix region as rpoB compensatory mutations previously described in Salmonella. Compared with the rpoB single-mutant BCG, the double mutant displayed improved growth characteristics and fitness rates equivalent to WT BCG. Strikingly, the rpoB double mutation conferred high-level resistance to rifampicin. CONCLUSIONS Here, we demonstrated the fitness compensatory role of a mutation within rpoB, secondary to the rifampicin resistance mutation rpoB S531L, which is characteristic of an MDR M. tuberculosis major outbreak strain. The finding that this secondary mutation concomitantly increased the resistance level to rifampicin argues for its significant contribution to the successful transmission of the MDR-TB strain.
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Affiliation(s)
- Nedra Meftahi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Amine Namouchi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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13
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Ifticene M, Kaïdi S, Khechiba MM, Yala D, Boulahbal F. Genetic diversity of Mycobacterium tuberculosis strains isolated in Algeria: Results of spoligotyping. Int J Mycobacteriol 2015; 4:290-5. [PMID: 26964810 DOI: 10.1016/j.ijmyco.2015.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 06/28/2015] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVE/BACKGROUND Molecular typing tools, including spoligotyping, are currently widely used in the monitoring and study of the dynamics of tuberculosis epidemics. METHODS A study of the molecular profile of a sample of 129 Myobacterium tuberculosis strains isolated during 2011 was carried out in the National Reference Laboratory for Tuberculosis and Mycobacteria at the Pasteur Institute of Algeria. This sample was selected at random from a set of 350 strains isolated from tuberculosis patients from central and eastern areas of the country. RESULTS Genotypic analysis helped to clarify the frequencies of the different genotypes in the current study population: H family, 29%; LAM family, 26%; T family, 25%; S family, 5%, and other genomic families, including orphan strains, 15%. CONCLUSION The study of strains isolated between January and December 2011 has allowed insight into the frequency of different genomic families and the importance of existing clusters in the population of central and eastern Algeria.
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Affiliation(s)
- Malika Ifticene
- National Reference Laboratory for Tuberculosis (NRL-TB), Pasteur Institute of Algeria, Algiers, Algeria.
| | - Saïd Kaïdi
- Department of Genetics & Physiology, Faculty of Agro-veterinary and Biological Sciences, Saad Dahlab University of Blida, Blida, Algeria
| | - Mesbah-Mounir Khechiba
- Department of Genetics & Physiology, Faculty of Agro-veterinary and Biological Sciences, Saad Dahlab University of Blida, Blida, Algeria
| | - Djamel Yala
- National Reference Laboratory for Tuberculosis (NRL-TB), Pasteur Institute of Algeria, Algiers, Algeria
| | - Fadila Boulahbal
- National Reference Laboratory for Tuberculosis (NRL-TB), Pasteur Institute of Algeria, Algiers, Algeria
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14
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Thabet S, Karboul A, Dekhil N, Mardassi H. IS6110-5'3'FP: an automated typing approach for Mycobacterium tuberculosis complex strains simultaneously targeting and resolving IS6110 5' and 3' polymorphisms. Int J Infect Dis 2014; 29:211-8. [PMID: 25447727 DOI: 10.1016/j.ijid.2014.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 10/18/2014] [Accepted: 10/18/2014] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Fingerprinting of Mycobacterium tuberculosis complex strains based on the IS6110 insertion sequence would considerably gain in terms of discriminatory power and versatility if both 5' and 3' polymorphisms were simultaneously targeted, and if it benefited from automated capillary electrophoresis. In response to these requirements, we developed IS6110-5'3'FP (IS6110 5' and 3' fluorescent polymorphisms). METHODS IS6110-5'3'FP involves the construction of an M. tuberculosis genomic library in a plasmid vector using HincII endonuclease, which cuts within the IS6110 sequence. After amplification in Escherichia coli, the library is subjected to selective and simultaneous PCR amplification of IS6110 5' and 3' polymorphic fragments, using differentially labeled fluorescent primers. The resulting amplicons are then fractionated on a capillary sequencer and the signal peaks analyzed as digital data. RESULTS IS6110-5'3'FP consistently detected and resolved both 5' and 3' IS6110 polymorphic fragments (35% and 65%, respectively) with a high level of reproducibility. The method differentiated all M. tuberculosis strains, as did IS6110 restriction fragment length polymorphism (RFLP), the gold standard of IS6110-based typing. Strikingly, the potential of IS6110-5'3'FP to resolve more polymorphic fragments than IS6110 RFLP was demonstrated. CONCLUSIONS IS6110-5'3'FP demonstrated sufficient potential to be a promising automated alternative to IS6110 RFLP, amenable to high throughput analysis and inter-laboratory comparison.
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Affiliation(s)
- Sara Thabet
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Anis Karboul
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Neira Dekhil
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, LR11IPT01 Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP 74, 1002, Tunis-Belvédère, Tunis, Tunisia.
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15
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Lahlou O, Millet J, Chaoui I, Sabouni R, Filali-Maltouf A, Akrim M, El Mzibri M, Rastogi N, El Aouad R. The genotypic population structure of Mycobacterium tuberculosis complex from Moroccan patients reveals a predominance of Euro-American lineages. PLoS One 2012; 7:e47113. [PMID: 23077552 PMCID: PMC3471964 DOI: 10.1371/journal.pone.0047113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 09/12/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) remains a major health problem in Morocco. Characterization of circulating Mycobacterium tuberculosis genotypic lineages, important to understand the dynamic of the disease, was hereby addressed for the first time at a national level. METHODOLOGY/PRINCIPAL FINDINGS Spoligotyping was performed on a panel of 592 M. tuberculosis complex strains covering a 2-year period (2004-2006). It identified 129 patterns: 105 (n = 568 strains) corresponded to a SIT number in the SITVIT2 database, while 24 patterns were labeled as orphan. A total of 523 (88.3%) strains were clustered vs. 69 or 11.7% unclustered. Classification of strains within 3 large phylogenetical groups was as follows: group 1- ancestral/TbD1+/PGG1 (EAI, Bovis, Africanum), group 2- modern/TbD1-/PGG1 group (Beijing, CAS), group 3- evolutionary recent/TbD1-/PGG2/3 (Haarlem, X, S, T, LAM; alternatively designated as the Euro-American lineage). As opposed to group 3 strains (namely LAM, Haarlem, and T) that predominated (86.5% of all isolates), 6 strains belonged to group 2 (Beijing n = 5, CAS n = 1), and 3 strains (BOV_1 n = 2, BOV_4-CAPRAE) belonged to ancestral group 1 (EAI and AFRI lineage strains were absent). 12-loci MIRU-VNTR typing of the Casablanca subgroup (n = 114 strains) identified 71 patterns: 48 MITs and 23 orphan patterns; it allowed to reduce the clustering rate from 72.8% to 29.8% and the recent transmission rate from 64% to 20.2%. CONCLUSION The M. tuberculosis population structure in Morocco is highly homogeneous, and is characterized by the predominance of the Euro-American lineages, namely LAM, Haarlem, and T, which belong to the "evolutionary recent" TbD1-/PGG2/3 phylogenetic group. The combination of spoligotyping and MIRUs decreased the clustering rate significantly, and should now be systematically applied in larger studies. The methods used in this study appear well suited to monitor the M. tuberculosis population structure for an enhanced TB management program in Morocco.
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Affiliation(s)
- Ouafae Lahlou
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Julie Millet
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Imane Chaoui
- Biology and Medical Research Unit, National Centre of Energy, Nuclear Sciences and Techniques, Rabat, Morocco
| | - Radia Sabouni
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University of Mohammed V-Agdal, Rabat, Morocco
| | - Mohammed Akrim
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Mohammed El Mzibri
- Biology and Medical Research Unit, National Centre of Energy, Nuclear Sciences and Techniques, Rabat, Morocco
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Rajae El Aouad
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
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16
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Mokrousov I. The quiet and controversial: Ural family of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:619-29. [PMID: 22036706 DOI: 10.1016/j.meegid.2011.09.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 12/15/2022]
Abstract
The absence of lateral gene exchange is a characteristic feature defining the genome evolution and clonal population structure of Mycobacterium tuberculosis. Certain of its lineages have justly attracted more attention due to their global dissemination and/or remarkable pathogenic properties. In this critical review, I discuss the population structure and genetic geography of the less 'popular' but in some aspects no less noteworthy M. tuberculosis lineage, Ural family. Its specific signature was initially defined by single copy in MIRU26, and large (>6) copy number in MIRU10 loci, and by 43-spoligotyping as absence of signals 29-31 and 33-36. Here, I suggest to subdivide Ural strains with present and absent spoligosignal 2 into primary Ural-1 and secondary Ural-2 sublineages, respectively, while 1 copy in MIRU26 is specific of Ural-1. Furthermore, three copies were recently described in MIRU10 in Ural-1 strains which highlights a high diversity of this locus in Ural genotype. The data on the two Ural sublineages were extracted from SpolDB4 database and original publications in order to trace their distribution at global and within-country levels. Importantly, the rigorous reanalysis suggested the true rate of the Ural genotype in the Ural area in Russia to be only 7%. In contrast, the frequencies of the Ural sublineages peak elsewhere: in South Ukraine and Georgia/Abkhazia (Ural-1, up to 14-19%), and in southwestern Iran (Ural-2, up to 26%). However, as this name is used since 2005, it seems most parsimonious to continue its use even if misleading. The forest graph was built on the available spoligoprofiles of Ural family strains from Eurasia. It helped to suggest routes of their primary dispersal that are discussed in the context of the known human migrations also influenced by natural barriers. The north/east Pontic area may have been an area of origin and primary dispersal of the Ural (Ural-1) genotype in Eurasia, whereas political and natural borders may have influenced its subsequent dissemination throughout Central Asia. Studies of phenotypic properties in different models, comparison with host genetics give evidence that the Ural family strains are not associated with increased capacity to acquire drug resistance, pathogenicity or transmissibility. Instead since Ural family is rather moderately widespread in Eurasia beyond the hypothesized areas of origin, this situation may be a result of its low contagiosity as a consequence of long-term co-adaptation with human host. Future research should be focused on whole-genome sequencing in order to identify Ural-specific SNP and/or deletion, to resolve its phylogenetic and phylogeographic uncertainty and to elucidate biological features underlying its circulation and co-evolution with the human species.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
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17
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Mycobacterium tuberculosis Complex Genotype Diversity and Drug Resistance Profiles in a Pediatric Population in Mexico. Tuberc Res Treat 2011; 2011:239042. [PMID: 22567263 PMCID: PMC3335619 DOI: 10.1155/2011/239042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/22/2011] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to determine the frequency of drug resistance and the clonality of genotype patterns in M. tuberculosis clinical isolates from pediatric patients in Mexico (n = 90 patients from 19 states; time period—January 2002 to December 2003). Pulmonary disease was the most frequent clinical manifestation (71%). Children with systemic tuberculosis (TB) were significantly younger compared to patients with localized TB infections (mean 7.7 ± 6.2
years versus 15 ± 3.4
years P = 0.001). Resistance to any anti-TB drug was detected in 24/90 (26.7%) of the isolates; 21/90 (23.3%) and 10/90 (11.1%) were resistant to Isoniazid and Rifampicin, respectively, and 10/90 (11.1%) strains were multidrug-resistant (MDR). Spoligotyping produced a total of 55 different patterns; 12/55 corresponded to clustered isolates (n = 47, clustering rate of 52.2%), and 43/55 to unclustered isolates (19 patterns were designated as orphan by the SITVIT2 database). Database comparison led to designation of 36 shared types (SITs); 32 SITs (n = 65
isolates) matched a preexisting shared type in SITVIT2, whereas 4 SITs (n = 6
isolates) were newly created. Lineage classification based on principal genetic groups (PGG) revealed that 10% of the strains belonged to PGG1 (Bovis and Manu lineages). Among PGG2/3 group, the most predominant clade was the Latin-American and Mediterranean (LAM) in 27.8% of isolates, followed by Haarlem and T lineages. The number of single drug-resistant (DR) and multidrug-resistant (MDR-TB) isolates in this study was similar to previously reported in studies from adult population with risk factors. No association between the spoligotype, age, region, or resistance pattern was observed. However, contrary to a study on M. tuberculosis spoligotyping in Acapulco city that characterized a single cluster of SIT19 corresponding to the EAI2-Manila lineage in 70 (26%) of patients, not a single SIT19 isolate was found in our pediatric patient population. Neither did we find any shared type belonging to the EAI family which represents ancestral PGG1 strains within the M. tuberculosis complex. We conclude that the population structure of pediatric TB in our setting is different from the one prevailing in adult TB patient population of Guerrero.
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18
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Groenheit R, Ghebremichael S, Svensson J, Rabna P, Colombatti R, Riccardi F, Couvin D, Hill V, Rastogi N, Koivula T, Källenius G. The Guinea-Bissau family of Mycobacterium tuberculosis complex revisited. PLoS One 2011; 6:e18601. [PMID: 21533101 PMCID: PMC3080393 DOI: 10.1371/journal.pone.0018601] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 03/07/2011] [Indexed: 11/19/2022] Open
Abstract
The Guinea-Bissau family of strains is a unique group of the Mycobacterium tuberculosis complex that, although genotypically closely related, phenotypically demonstrates considerable heterogeneity. We have investigated 414 M. tuberculosis complex strains collected in Guinea-Bissau between 1989 and 2008 in order to further characterize the Guinea-Bissau family of strains. To determine the strain lineages present in the study sample, binary outcomes of spoligotyping were compared with spoligotypes existing in the international database SITVIT2. The major circulating M. tuberculosis clades ranked in the following order: AFRI (n = 195, 47.10%), Latin-American-Mediterranean (LAM) (n = 75, 18.12%), ill-defined T clade (n = 53, 12.8%), Haarlem (n = 37, 8.85%), East-African-Indian (EAI) (n = 25, 6.04%), Unknown (n = 12, 2.87%), Beijing (n = 7, 1.68%), X clade (n = 4, 0.96%), Manu (n = 4, 0.97%), CAS (n = 2, 0.48%). Two strains of the LAM clade isolated in 2007 belonged to the Cameroon family (SIT61). All AFRI isolates except one belonged to the Guinea-Bissau family, i.e. they have an AFRI_1 spoligotype pattern, they have a distinct RFLP pattern with low numbers of IS6110 insertions, and they lack the regions of difference RD7, RD8, RD9 and RD10, RD701 and RD702. This profile classifies the Guinea-Bissau family, irrespective of phenotypic biovar, as part of the M. africanum West African 2 lineage, or the AFRI_1 sublineage according to the spoligtyping nomenclature. Guinea-Bissau family strains display a variation of biochemical traits classically used to differentiate M. tuberculosis from M. bovis. Yet, the differential expression of these biochemical traits was not related to any genes so far investigated (narGHJI and pncA). Guinea-Bissau has the highest prevalence of M. africanum recorded in the African continent, and the Guinea-Bissau family shows a high phylogeographical specificity for Western Africa, with Guinea-Bissau being the epicenter. Trends over time however indicate that this family of strains is waning in most parts of Western Africa, including Guinea-Bissau (p = 0.048).
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Affiliation(s)
- Ramona Groenheit
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Solomon Ghebremichael
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Jenny Svensson
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Paulo Rabna
- Laboratório Nacional de Saúde Pública, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Raffaella Colombatti
- Hospital “Raoul Follereau”, Bissau, Guinea-Bissau
- Department of Pediatrics, Azienda Ospedaliera-Università di Padova, Padova, Italy
| | - Fabio Riccardi
- Department of Public Health, University of “Tor Vergata”, Rome, Italy
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Véronique Hill
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Tuberculosis and Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Tuija Koivula
- Department of Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Källenius
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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García de Viedma D, Mokrousov I, Rastogi N. Innovations in the molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin 2011; 29 Suppl 1:8-13. [DOI: 10.1016/s0213-005x(11)70012-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Spoligotype profile of Mycobacterium tuberculosis complex strains from HIV-positive and -negative patients in Nigeria: a comparative analysis. J Clin Microbiol 2010; 49:220-6. [PMID: 21048016 DOI: 10.1128/jcm.01241-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We ran a comparative analysis of all patients for whom a positive culture of Mycobacterium tuberculosis complex was available between April 2004 and October 2005 and whose HIV serology results were known, with spoligotyping results (n = 163) split into 49 HIV-positive patients and 114 HIV-negative patients. Spoligotype international type 373 (SIT373) (T1 lineage), which was highly prevalent among the HIV(+) patients, was totally absent from the HIV(-) population, suggesting that we had a specific clone affecting nearly 1/3 of all HIV-tuberculosis (TB)-coinfected patients. Among the LAM10-CAM sublineage strains, we had only a single strain of SIT403 among HIV(-) patients (0.88%), as opposed to 12.25% of the HIV(+) population (χ(2) = 10.77; P < 0.01), indicating a strong association between the strain and the HIV(+) population. The LAM10-CAM lineage spoligotype SIT61 was prevalent among the 2 subsets (37.72% in HIV(-) versus 12.24% in HIV(+) populations), though, with a significant difference between the 2 groups (χ(2) = 10.53; P < 0.01). However, there was no significant difference for SIT53 (T1 lineage) in the 2 subsets: 6.14 versus 8.2% (χ(2) = 0.22; P > 0.05). A total of 7/49, or 14.3%, other SITs among HIV(+) patients were not found among the HIV(-) patients. When added to the most prevalent SIT among HIV(+) patients (SIT373; n = 16), 23/49, or 47%, isolates among HIV-TB-coinfected patients were unique. We conclude that further studies should be carried out to investigate the evolution of these genotypes and others in the emergence of multidrug resistance and control of tuberculosis in Nigeria.
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Valcheva V, Mokrousov I, Panaiotov S, Bachiiska E, Zozio T, Sola C, Markova N, Rastogi N. Bulgarian specificity and controversial phylogeography of Mycobacterium tuberculosis spoligotype ST 125__BGR. ACTA ACUST UNITED AC 2010; 59:90-9. [PMID: 20402768 DOI: 10.1111/j.1574-695x.2010.00667.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The local specificity of bacterial clones may be explained by long-term presence or recent importation/fast dissemination in an area. Mycobacterium tuberculosis spoligotype ST125, noticeably prevalent among Bulgaria-specific spoligotypes, has a characteristically 'abridged' profile and an uncertain clade position [Latin-American-Mediterranean (LAM)/S]. A comparison with the SITVIT2 database (Institut Pasteur de Guadeloupe) demonstrated its high gradient in Bulgaria (14.3%) compared with the negligible presence in the rest of the world. Further typing of all available Bulgarian ST125 strains revealed that they: (i) monophyletically clustered in 21-mycobacterial interspersed repetitive units (MIRU)-loci tree of all Bulgarian strains; (ii) grouped closely with the ST34 spoligotype, a prototype of the S family; and (iii) did not harbor a LAM-specific IS6110 insertion. Comparison of the 21-MIRU-based network with geographic data revealed a complex dissemination pattern of ST125 in Bulgaria. Interestingly, this variable number of tandem repeats (VNTR) network remarkably corroborated with a recent hypothesis of single repeat loss as the primary mode of evolution of VNTR loci in M. tuberculosis. In conclusion, M. tuberculosis spoligotype ST125 is phylogeographically specific for Bulgaria. This spoligotype was not associated with drug resistance or increased transmissibility; its prevalence in Bulgaria can rather be attributed to the historical circulation in the country, having led, speculatively, to adaptation to the local human population.
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Affiliation(s)
- Violeta Valcheva
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe, France
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Pepperell C, Hoeppner VH, Lipatov M, Wobeser W, Schoolnik GK, Feldman MW. Bacterial genetic signatures of human social phenomena among M. tuberculosis from an Aboriginal Canadian population. Mol Biol Evol 2009; 27:427-40. [PMID: 19861642 DOI: 10.1093/molbev/msp261] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Despite a widespread global distribution and highly variable disease phenotype, there is little DNA sequence diversity among isolates of Mycobacterium tuberculosis. In addition, many regional population genetic surveys have revealed a stereotypical structure in which a single clone, lineage, or clade makes up the majority of the population. It is often assumed that dominant clones are highly adapted, that is, the overall structure of M. tuberculosis populations is the result of positive selection. In order to test this assumption, we analyzed genetic data from extant populations of bacteria circulating in Aboriginal communities in Saskatchewan, Canada. Demographic parameters of the bacterial population were estimated from archival epidemiological data collected over approximately 130 years since the onset of epidemic tuberculosis in the host communities. Bacterial genetic data were tested against neutral theory expectations and the local evolutionary history of M. tuberculosis investigated by phylogenetic analysis. Our findings are not consistent with positive selection on the bacterial population. Instead, we uncovered founder effects persisting over decades and barriers to gene flow within the bacterial population. Simulation experiments suggested that a combination of these neutral influences could result in the stereotypical structure of M. tuberculosis populations. Some aspects of population structure were suggestive of background selection, and data were on the whole consistent with combined effects of population bottlenecks, subdivision, and background selection. Neutral phenomena, namely, bottlenecks and partitions within populations, are prominent influences on the evolution of M. tuberculosis and likely contribute to restricted genetic diversity observed within this species. Given these influences, a complex evolutionary model will be required to define the relative fitness of different M. tuberculosis lineages and, ultimately, to uncover the genetic basis for its success as a pathogen.
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Unexpectedly high proportion of ancestral Manu genotype Mycobacterium tuberculosis strains cultured from tuberculosis patients in Egypt. J Clin Microbiol 2009; 47:2794-801. [PMID: 19553569 DOI: 10.1128/jcm.00360-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Tuberculosis is one of the important public health problems in Egypt. However, limited information on the Mycobacterium tuberculosis genotypes circulating in Egypt is available. A total of 151 M. tuberculosis strains were characterized by spoligotyping. The results revealed that 74.8% of M. tuberculosis isolates grouped into 13 different clusters, while 25.2% had unique spoligotype patterns. Comparison with an international spoligotyping database (the SITVIT2 database) showed that types SIT53 (T1 variant) and SIT54 (Manu2 variant) were the most common types between cluster groups. In addition, new shared types SIT2977, SIT2978, and SIT2979 were observed. The results identified for the first time an unusually high proportion of ancestral Manu strains of M. tuberculosis from patients in Egypt. The percentage of the Manu clade in this study (27.15%) was significantly higher than its overall representation of 0.4% in the SITVIT2 database. We show that in Egypt tuberculosis is caused by a predominant M. tuberculosis genotype belonging to the ancestral Manu lineage which could be a missing link in the split between ancestral and modern tubercle bacilli during the evolution of M. tuberculosis.
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Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: potential role in antigenic variability. J Bacteriol 2008; 190:7838-46. [PMID: 18820012 DOI: 10.1128/jb.00827-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PE and PPE (PE/PPE) multigene families of Mycobacterium tuberculosis are particularly GC-rich and share extensive homologous repetitive sequences. We hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. To test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the PE/PPE genes, aimed at detecting signals for homologous recombination. Such a microarray has never before been reported due to the multiplicity and highly repetitive and homologous nature of these sequences. Application of the microarray to a collection of M. tuberculosis clinical isolates (n = 33) representing prevalent spoligotype strain families in Tunisia allowed successful detection of six deleted genomic regions involving a total of two PE and seven PPE genes. Some of these deleted genes are known to be immunodominant or involved in virulence. The four precisely determined deletions were flanked by 400- to 500-bp stretches of nearly identical sequences lying mainly at the conserved N-terminal region of the PE/PPE genes. These highly homologous sequences thus serve as substrates to mediate both intergenic and intragenic homologous recombination events, indicating an important function in generating strain variation. Importantly, all recombination events yielded a new in-frame fusion chimeric gene. Hence, homologous recombination within and between PE/PPE genes likely increased their antigenic variability, which may have profound implications in pathogenicity and/or host adaptation. The finding of high prevalence (approximately 45% and approximately 58%) for at least two of the genomic deletions suggests that they likely confer advantageous biological attributes.
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