1
|
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.
Collapse
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;
| |
Collapse
|
2
|
Bouklata N, Supply P, Jaouhari S, Charof R, Seghrouchni F, Sadki K, El Achhab Y, Nejjari C, Filali-Maltouf A, Lahlou O, El Aouad R. Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco. PLoS One 2015; 10:e0135695. [PMID: 26285026 PMCID: PMC4540494 DOI: 10.1371/journal.pone.0135695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/26/2015] [Indexed: 01/27/2023] Open
Abstract
Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context.
Collapse
Affiliation(s)
- Nada Bouklata
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
- * E-mail:
| | - Philip Supply
- INSERMU1018, Lille, France
- CNRS UMR8204, Lille, France
- Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, France
- Université de Lille, Lille, France
- Genoscreen, Lille, France
| | - Sanae Jaouhari
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Reda Charof
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Fouad Seghrouchni
- Laboratory of Cell Immunology, Department of Immunology, National Institute of Hygiene, Rabat, Morocco
| | - Khalid Sadki
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Youness El Achhab
- Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco
| | - Chakib Nejjari
- Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Ouafae Lahlou
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Rajae El Aouad
- School of Public Health and Management System Health, University Mohamed VI of Sciences and Health, Casablanca, Morocco
| |
Collapse
|
3
|
Panaiotov S, Bachiyska E, Yordanova S, Atanasova Y, Brankova N, Levterova V, Sengstake S, Anthony R, Bergval I, Sola C, Kantardjiev T. Beijing lineage of MDR Mycobacterium tuberculosis in Bulgaria, 2007-2011. Emerg Infect Dis 2014; 20:1899-901. [PMID: 25340498 PMCID: PMC4214304 DOI: 10.3201/eid2011.140468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To assess the spread of the Mycobacterium tuberculosis Beijing genotype among patients with multidrug-resistant and extensively resistant tuberculosis in Bulgaria, we genotyped 188 (72%) of 261 microbiologically confirmed resistant isolates obtained during 2007–2011. The estimated prevalence of the Beijing genotype among these patients was 3.2%.
Collapse
|
4
|
Boyanova L, Davidkov L, Gergova G, Kandilarov N, Evstatiev I, Panteleeva E, Mitov I. Helicobacter pylori susceptibility to fosfomycin, rifampin, and 5 usual antibiotics for H. pylori eradication. Diagn Microbiol Infect Dis 2014; 79:358-61. [DOI: 10.1016/j.diagmicrobio.2014.03.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/25/2014] [Accepted: 03/29/2014] [Indexed: 12/14/2022]
|
5
|
Chaoui I, Zozio T, Lahlou O, Sabouni R, Abid M, El Aouad R, Akrim M, Amzazi S, Rastogi N, El Mzibri M. Contribution of spoligotyping and MIRU-VNTRs to characterize prevalent Mycobacterium tuberculosis genotypes infecting tuberculosis patients in Morocco. INFECTION GENETICS AND EVOLUTION 2013; 21:463-71. [PMID: 23732366 DOI: 10.1016/j.meegid.2013.05.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/30/2013] [Accepted: 05/23/2013] [Indexed: 11/28/2022]
Abstract
In the present study, Mycobacterium tuberculosis complex (MTBC) clinical isolates from culture-positive TB patients in Morocco were studied by spoligotyping and 12-loci MIRU-VNTR typing methods to characterize prevalent genotypes (n = 219 isolates from 208 patients). Spoligotyping resulted in 39 unique patterns and 167 strains in 30 clusters (2-50 strains per cluster). Comparison with international database showed that 29 of 39 unique patterns matched existing shared spoligotype international types (SITs). Nine shared types containing 10 strains were newly created (SIT 2891 to SIT 2899); this led to the description of 69 SITs with 206 strains and two orphan patterns. The most prevalent spoligotype was SIT42 (LAM; n = 50 or 24% of isolates). The repartition of strains according to major MTBC clades was as follows LAM (46.1%)> Haarlem (26%) >ill-defined T superfamily (22.6%) and S clade (0.96%). On the other hand, Beijing, CAS (Central Asian) and EAI (East-African Indian) strains were absent in this setting. Subsequent 12-Loci MIRU typing resulted in a total of 25 SIT/MIT clusters (n = 66 isolates, 2-6 isolates per cluster), with a resulting recent transmission rate of 22.3%. The MIRU-VNTR patterns corresponded to 69 MITs for 138 strains and 46 orphan patterns. The most frequent patterns were MIT43 (n = 8), MIT9 (n = 7) and MIT42 (n = 7). HGDI analysis of the 12 MIRU loci showed that loci 10, 23 and 40 were highly discriminative in our setting. The results also underlined the usefulness of spoligotyping and MIRU-VNTR to detect mixed infections among certain of our TB patients. Globally, the results obtained showed that TB is almost exclusively transmitted in Morocco through evolutionary-modern MTBC lineages belonging to principal genetic groups 2/3 strains (Haarlem, LAM, T), with a high level of biodiversity seen by MIRU typing. This study provides with a 1st global snapshot of MTBC population structure in Morocco, and validates the potential use of spoligotyping in conjunction with minisatellites for future investigations in Morocco that should in future ideally include optimized 15- or 24-loci MIRU-VNTRs.
Collapse
Affiliation(s)
- Imane Chaoui
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, Rabat, Morocco.
| | - Thierry Zozio
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, F97183 Abymes, Guadeloupe, France
| | - Ouafae Lahlou
- Laboratoire de Référence de la Tuberculose, Institut National d'Hygiène, Rabat, Morocco
| | - Radia Sabouni
- Laboratoire de Référence de la Tuberculose, Institut National d'Hygiène, Rabat, Morocco
| | - Mohammed Abid
- Laboratoire de génétiques des mycobactéries, service de Recherches, Institut Pasteur, Tanger, Morocco
| | - Rajae El Aouad
- Laboratoire de Référence de la Tuberculose, Institut National d'Hygiène, Rabat, Morocco; Laboratoire de biologie moléculaire, Institut National d'Hygiène, Rabat, Morocco
| | - Mohammed Akrim
- Laboratoire de biologie moléculaire, Institut National d'Hygiène, Rabat, Morocco
| | - Said Amzazi
- Laboratoire de biochimie et Immunologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, F97183 Abymes, Guadeloupe, France.
| | - Mohammed El Mzibri
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, Rabat, Morocco
| |
Collapse
|
6
|
Ragheb MN, Ford CB, Chase MR, Lin PL, Flynn JL, Fortune SM. The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection. BMC Genomics 2013; 14:145. [PMID: 23496945 PMCID: PMC3635867 DOI: 10.1186/1471-2164-14-145] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/26/2013] [Indexed: 11/25/2022] Open
Abstract
Background Mycobacterial interspersed repetitive units (MIRUs) are minisatellites within the Mycobacterium tuberculosis (Mtb) genome. Copy number variation (CNV) in MIRU loci is used for epidemiological typing, making the rate of variation important for tracking the transmission of Mtb strains. In this study, we developed and assessed a whole-genome sequencing (WGS) approach to detect MIRU CNV in Mtb. We applied this methodology to a panel of Mtb strains isolated from the macaque model of tuberculosis (TB), the animal model that best mimics human disease. From these data, we have estimated the rate of MIRU variation in the host environment, providing a benchmark rate for future epidemiologic work. Results We assessed variation at the 24 MIRU loci used for typing in a set of Mtb strains isolated from infected cynomolgus macaques. We previously performed WGS of these strains and here have applied both read depth (RD) and paired-end mapping (PEM) metrics to identify putative copy number variants. To assess the relative power of these approaches, all MIRU loci were resequenced using Sanger sequencing. We detected two insertion/deletion events both of which could be identified as candidates by PEM criteria. With these data, we estimate a MIRU mutation rate of 2.70 × 10-03 (95% CI: 3.30 × 10-04- 9.80 × 10-03) per locus, per year. Conclusion Our results represent the first experimental estimate of the MIRU mutation rate in Mtb. This rate is comparable to the highest previous estimates gathered from epidemiologic data and meta-analyses. Our findings allow for a more rigorous interpretation of data gathered from MIRU typing.
Collapse
Affiliation(s)
- Mark N Ragheb
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | | | | | | | | | | |
Collapse
|
7
|
Pang Y, Zhou Y, Wang S, Lu J, Lu B, He G, Wang L, Zhao Y. A novel method based on high resolution melting (HRM) analysis for MIRU–VNTR genotyping of Mycobacterium tuberculosis. J Microbiol Methods 2011; 86:291-7. [DOI: 10.1016/j.mimet.2011.05.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/16/2011] [Accepted: 05/26/2011] [Indexed: 01/07/2023]
|
8
|
Dymova MA, Liashenko OO, Poteiko PI, Krutko VS, Khrapov EA, Filipenko ML. Genetic variation of Mycobacterium tuberculosis circulating in Kharkiv Oblast, Ukraine. BMC Infect Dis 2011; 11:77. [PMID: 21439097 PMCID: PMC3079650 DOI: 10.1186/1471-2334-11-77] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 03/28/2011] [Indexed: 11/10/2022] Open
Abstract
Background A persistent increase of tuberculosis cases has recently been noted in the Ukraine. The reported incidence of drug-resistant isolates of M. tuberculosis is growing steadily; however, data on the genetic variation of isolates of M. tuberculosis circulating in northern Ukraine and on the spectrum and frequency of occurrence of mutations determining resistance to the principal anti-tuberculosis drugs isoniazid and rifampicin have not yet been reported. Methods Isolates of M. tuberculosis from 98 tuberculosis patients living in Kharkiv Oblast (Ukraine) were analyzed using VNTR- and RFLP-IS6110-typing methods. Mutations associated with resistance to rifampicin and isoniazid were detected by RFLP-PCR methods, and also confirmed by sequencing. Results We identified 75 different genetic profiles. Thirty four (34%) isolates belonged to the Beijing genotype and 23 (23%) isolates belonged to the LAM family. A cluster of isolates belonging to the LAM family had significant genetic heterogeneity, indicating that this family had an ancient distribution and circulation in this geographical region. Moreover, we found a significant percentage of the isolates (36%) belonged to as yet unidentified families of M. tuberculosis or had individual non-clustering genotypes. Mutations conferring rifampicin and isoniazid resistance were detected in 49% and 54% isolates, respectively. Mutations in codon 531 of the rpoB gene and codon 315 of the katG gene were predominant among drug-resistant isolates. An association was found for belonging to the LAM strain family and having multiple drug resistance (R = 0.27, p = 0.0059) and also for the presence of a mutation in codon 531 of the rpoB gene and belonging to the Beijing strain family (R = 0.2, p = 0.04). Conclusions Transmission of drug-resistant isolates seems to contribute to the spread of resistant TB in this oblast. The Beijing genotype and LAM genotype should be seen as a major cause of drug resistant TB in this region.
Collapse
Affiliation(s)
- Maya A Dymova
- Institute of Chemical Biology and Basic Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russian Federation, Russia.
| | | | | | | | | | | |
Collapse
|
9
|
Noguti EN, Leite CQF, Malaspina AC, Santos ACB, Hirata RDC, Hirata MH, Mamizuka EM, Cardoso RF. Genotyping of Mycobacterium tuberculosis isolates from a low-endemic setting in northwestern state of Paraná in Southern Brazil. Mem Inst Oswaldo Cruz 2011; 105:779-85. [PMID: 20944992 DOI: 10.1590/s0074-02762010000600008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/13/2010] [Indexed: 11/22/2022] Open
Abstract
The purpose of this study was to provide information about the genetic diversity and prevalent genotype of Mycobacterium tuberculosis in a low-endemic setting in northwestern state of Paraná in Southern Brazil. We employed spoligotyping and mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) techniques to genotype M. tuberculos isisolates from patients with pulmonary tuberculosis (TB). The 93 isolates analyzed by spoligotyping were divided into 36 different patterns, 30 of which were described in the SITVIT database. Latin American and Mediterranean, Haarlem and T families were responsible for 26.9%, 17.2% and 11.8% of TB cases, respectively. From the 84 isolates analyzed by MIRU-VNTR, 58 shared a unique pattern and the remaining 26 belonged to nine clusters. The MIRU loci 40, 23, 10 and 16 were the most discriminatory. A combination of MIRU-VNTR and spoligotyping resulted in 85.7% discriminatory power (Hunter-Gaston index = 0.995). Thus, combining spoligotyping and MIRU-VNTR typing proved to be most useful for epidemiological study in this low-endemic setting in Southern Brazil. The current study demonstrated that there is significant diversity in circulating strains in the city of Maringá and the surrounding regions, with no single genotype of M. tuberculosis predominating.
Collapse
Affiliation(s)
- Erika Noda Noguti
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Violeta Valcheva
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe, France
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Zhang J, Abadia E, Refregier G, Tafaj S, Boschiroli ML, Guillard B, Andremont A, Ruimy R, Sola C. Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay. J Med Microbiol 2009; 59:285-294. [PMID: 19959631 DOI: 10.1099/jmm.0.016949-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aims of the present study were to implement a microbead-based 'spoligotyping' technique and to evaluate improvements by the addition of a panel of 25 extra spacers that we expected to provide an increased resolution on principal genetic group 1 (PGG 1) strains. We confirmed the high sensitivity and reproducibility of the classical technique using the 43 spacer panel and we obtained perfect agreement between the membrane-based and the microbead-based techniques. We further demonstrated an increase in the discriminative power of an extended 68 spacer format for differentiation of PGG 1 clinical isolates, in particular for the East African-Indian clade. Finally, we define a limited yet highly informative reduced 10 spacer panel set which could offer a more cost-effective option for implementation in resource-limited countries and that could decrease the need for additional VNTR (variable number of tandem repeats) genotyping work in molecular epidemiological studies. We also present an economic analysis comparing membrane-based and microbead-based techniques.
Collapse
Affiliation(s)
- Jian Zhang
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Edgar Abadia
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Guislaine Refregier
- IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| | - Silva Tafaj
- National TB Reference Laboratory, University Hospital of Lung Diseases 'Shefqet Ndroqi', Tirana, Albania
| | | | | | - Antoine Andremont
- Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France
| | - Raymond Ruimy
- Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France
| | - Christophe Sola
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France.,IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France
| |
Collapse
|
12
|
Godreuil S, Renaud F, Choisy M, Depina JJ, Garnotel E, Morillon M, Van de Perre P, Bañuls AL. Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti. Clin Microbiol Infect 2009; 16:1023-6. [PMID: 19694762 DOI: 10.1111/j.1469-0691.2009.03025.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.
Collapse
Affiliation(s)
- S Godreuil
- Laboratoire de Bactériologie-Virologie Arnaud de Villeneuve, Université Montpellier 1, EA 4205 Transmission, Pathogenèse et Prévention de l'Infection par le VIH, and CHU Montpellier, Montpellier, France.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of beijing multidrug-resistant isolates. J Clin Microbiol 2009; 47:1581-4. [PMID: 19279172 DOI: 10.1128/jcm.02284-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized a set of 100 Mycobacterium tuberculosis complex clinical isolates from tuberculosis (TB) patients in Albania, typing them with a 24-locus variable-number tandem-repeat-spoligotyping scheme. Depending on the cluster definition, 43 to 49 patients were distributed into 15 to 16 clusters which were likely to be epidemiologically linked, indicative of a recent transmission rate of 28 to 34%. This result suggests that TB is under control in Albania. However, two multidrug-resistant (MDR) Beijing genotypes harboring the same S531A mutation on the rpoB gene were also found, suggesting a potential recent transmission of MDR TB. Three brand new genotypes, Albania-1 to Albania-3, are also described.
Collapse
|
14
|
Valcheva V, Mokrousov I, Narvskaya O, Rastogi N, Markova N. Molecular snapshot of drug-resistant and drug-susceptible Mycobacterium tuberculosis strains circulating in Bulgaria. INFECTION GENETICS AND EVOLUTION 2008; 8:657-63. [DOI: 10.1016/j.meegid.2008.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 11/26/2022]
|
15
|
Utility of new 24-locus variable-number tandem-repeat typing for discriminating Mycobacterium tuberculosis clinical isolates collected in Bulgaria. J Clin Microbiol 2008; 46:3005-11. [PMID: 18614651 DOI: 10.1128/jcm.00437-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study evaluated new markers for molecular typing of Mycobacterium tuberculosis with a collection of strains circulating in Bulgaria. A study sample included 133 strains from epidemiologically unlinked patients from different regions of the country. Spoligotyping was used as a primary typing tool; it subdivided these strains into 37 types, including 15 clusters and 22 singletons. Traditional IS6110-restriction fragment length polymorphism (RFLP) typing and novel 24-locus variable number tandem-repeat (VNTR) typing methods were applied to the selection of 73 strains. Discriminatory power (Hunter-Gaston index [HGI]) of these methods was found to be 0.983 and 0.997, respectively. The 73 strains were subdivided into 66 types by a 24-locus mycobacterial interspersed repetitive unit (MIRU)-VNTR scheme, 62 types by a classical 12-locus MIRU-VNTR scheme, 51 types by IS6110-RFLP typing, and 31 types by spoligotyping. A combination of the five most polymorphic loci (MIRU40, Mtub04, Mtub21, QUB-11b, and QUB-26) was shown to achieve a high discrimination (HGI = 0.984). To conclude, a complete 24-locus scheme excellently differentiated strains in our study, whereas a reduced 5-locus set provided a sufficiently high differentiation and may be preliminarily suggested for the first-line typing of M. tuberculosis isolates in Bulgaria.
Collapse
|