1
|
Benremila D, Djoudi F, Gharout-Sait A, Kheloufi S, Spitaleri A, Battaglia S, Cabibbe AM, Cirillo DM. Comprehensive Drug Resistance Characterization of Pulmonary Tuberculosis in Algeria: Insights on Mycobacterium tuberculosis Strains by Whole-Genome Sequencing. Microb Drug Resist 2023. [PMID: 37115530 DOI: 10.1089/mdr.2022.0321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
In this study, we aimed to characterize drug-resistant strains by whole-genome sequencing (WGS), to describe the spreading lineages and the history of transmission. Drug susceptibility testing was performed by 96-well broth microdilution plates. The genomic DNA was extracted and purified; libraries were prepared and run on the Illumina NextSeq500 System. Among 82 isolates, 21 tuberculosis (TB) isolates (25.6%) were drug resistant, including 10 MDR and 4 pre-extensively drug-resistant (XDR)-TB. The mutation Ser315Thr in the katG gene was confirmed in 15 isolates. In rpoB, Ser450Leu and His445Asp mutations were the most common. Asp94Asn and Ala90Val mutations were reported in gyrA. The LAM family, the most TB drug resistant, was widely predominant in the north and the T sublineage in the south of the country. This study provides the first insight on TB drug resistance using WGS in Algeria and clearly describes the first pre-XDR-TB cases and lineage distribution across the country.
Collapse
Affiliation(s)
- Dalila Benremila
- Laboratoire d'Écologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Route de Targa-Ouzemour, Université de Bejaia, Bejaia, Algeria
| | - Ferhat Djoudi
- Laboratoire d'Écologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Route de Targa-Ouzemour, Université de Bejaia, Bejaia, Algeria
| | - Alima Gharout-Sait
- Laboratoire d'Écologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Route de Targa-Ouzemour, Université de Bejaia, Bejaia, Algeria
| | - Slimane Kheloufi
- Laboratoire d'Écologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Route de Targa-Ouzemour, Université de Bejaia, Bejaia, Algeria
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Maurizio Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
2
|
Asgharzadeh M, Rashedi J, Poor BM, Kafil HS, Zadeh HM, Ahmadpour E. How Molecular Epidemiology Can Affect Tuberculosis Control in the Middle East Countries: A Systematic Review and Meta-Analysis. Infect Disord Drug Targets 2021; 21:28-37. [PMID: 31903887 DOI: 10.2174/1871526520666200106123619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/13/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nowadays, due to the incidence of specific strains of Mycobacterium tuberculosis and also an increase in the rate of drug resistant-TB, the mortality rate has been increased by this disease. The identification of common strains in the region, as well as the sources of transmission, is essential to control the disease, which is possible by using molecular epidemiology. OBJECTIVES In this survey, the studies utilizing the spoligotyping method in Muslim Middle East countries are reviewed to determine their role in the control of TB. METHODS All studies conducted from 2005 to June 2016 were considered systematically in three electronic databases out of which 23 studies were finally selected. RESULTS The average rate of clustering was 84% and the rate of recent transmission varied from 21.7% to 92.4%. The incidence of Beijing strains has been found to be rising in the abovementioned countries. In Iran and Saudi Arabia known as immigration and labour-hosting countries, respectively, rapid transmittable and drug-resistant Beijing strains were higher than those in other Muslim Middle East countries. CONCLUSION Considering the incidence of highly virulent strains, due to the increase in immigration and people infected with HIV, tuberculosis, especially drug-resistant form, careful monitoring is needed.
Collapse
Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavi Poor
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Moharram Zadeh
- Women's Reproduction Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsan Ahmadpour
- Department of Medical Parasitology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
3
|
Oudghiri A, Momen G, Aainouss A, Laglaoui A, El Messaoudi MD, El Mzibri M, Chaoui I. Genotypic diversity of multi- and pre-extremely drug-resistant Mycobacterium tuberculosis isolates from Morocco. PLoS One 2021; 16:e0253826. [PMID: 34214120 PMCID: PMC8253442 DOI: 10.1371/journal.pone.0253826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/13/2021] [Indexed: 12/02/2022] Open
Abstract
In Morocco, the prevalence of multidrug resistant tuberculosis (MDR-TB) continues to increase especially within previously treated cases; these MDR cases may evolve to extensively drug resistant tuberculosis (XDR-TB) raising major concern to TB control programs. From an epidemiological window, scarce informations are available about the genetic diversity of Mycobacterium tuberculosis (MTB) strains fueling these forms of resistance. The aim of this study was to assess to genetic diversity of MDR-MTB strains. Hence, this prospective study was conducted on patients diagnosed with MDR-TB at Pasteur Institute of Casablanca from 2010 to 2013. A total of 70 MDR-MTB isolates were genotyped by spoligotyping and 15-loci MIRU-VNTR methods. Spoligotyping generated four orphan patterns, five unique profiles whereas 61 strains were grouped in nine clusters (2 to 25 strains per cluster), the clustering rates being 87.1%. Subtyping by 15 loci MIRU-VNTR splitted all clusters already established by spoligotyping and generated 70 unique profiles not recognized in SITVIT2 database; clustering rate was equal to zero. HGDI analysis of 15 loci MIRU demonstrated that eight out of 15 loci were highly discriminant. Of note, all pre-XDR strains belongs to many clades, meaning that there no association between gyrA mutants and particular clade. Overall, the data generated by this study (i) describe the population structure of MDR MTBC in Morocco which is highly homogenous, (ii) confirm that TB in Morocco is almost exclusively transmitted by modern and evolutionary lineages with high level of biodiversity seen by MIRU, and (iii) validate the use of optimized 15-loci MIRU-VNTR format for future investigations in Morocco.
Collapse
Affiliation(s)
- Amal Oudghiri
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
- Faculty of Sciences and Techniques, Biotechnology and Bimolecular Engineering Research Laboratory, Tangier, Morocco
| | - Ghizlane Momen
- Laboratory of Mycabacteria, Pasteur Institute of Morocco, Casablanca, Morocco
- Faculty of Sciences, Laboratory of Microbiology Pharmacology, Biotechnology and Environment, Casablanca, Morocco
| | - Achraf Aainouss
- Laboratory of Mycabacteria, Pasteur Institute of Morocco, Casablanca, Morocco
- Faculty of Sciences Ben M’Sik, Laboratory of Ecology and Environment, Casablanca, Morocco
| | - Amin Laglaoui
- Faculty of Sciences and Techniques, Biotechnology and Bimolecular Engineering Research Laboratory, Tangier, Morocco
| | | | - Mohammed El Mzibri
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
| | - Imane Chaoui
- Department of Life Sciences, Medical and Biological Research Unit, National Center of Energy, Sciences and Nuclear Techniques, Rabat, Morocco
- * E-mail: ,
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
A molecular epidemiological analysis of tuberculosis trends in South Korea. Tuberculosis (Edinb) 2018; 111:127-134. [PMID: 30029897 DOI: 10.1016/j.tube.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/25/2018] [Accepted: 06/05/2018] [Indexed: 11/24/2022]
Abstract
Molecular epidemiological data are needed to assess tuberculosis (TB)-management policy outcomes in South Korea. IS6110 restriction fragment-length polymorphism (IS6110-RFLP) and mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) analyses are major molecular epidemiological tools for investigating the transmission or reactivation of active TB. Here, we determined trends in the clustering rate (i.e., the prevalence of Mycobacterium tuberculosis isolates with identical genotype patterns) of active TB and related differences between the 1990s and 2000s in Korea. M. tuberculosis isolates (1,007) of nationwide origins were analyzed by IS6110-RFLP and 24-locus standardized MIRU-VNTR genotyping. The clustering rate was measured by IS6110-RFLP, 24-locus MIRU-VNTR, and both analytical methods in combination. IS6110-RFLP, 24-locus MIRU-VNTR typing, and the combined method revealed 882, 754, and 983 distinct profiles; 809, 651, and 961 unique isolates; and 198, 356, and 46 clustered isolates grouped into 73, 103, and 22 clusters, respectively. In addition, we confirmed that the clustering rates in the 2000s decreased by 11.2%, 2.1%, and 3.1% relative to that in the 1990s using the three methods, respectively. Furthermore, in multivariate analysis, the younger-age group (<30) clustered more frequently than the older-age group (>50), based on all the three methods. Our study is the first report to provide nationwide molecular epidemiological information on TB in Korea.
Collapse
|
6
|
Pourostadi M, Rashedi J, Mahdavi Poor B, Samadi Kafil H, Shirazi S, Asgharzadeh M. Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran. Jundishapur J Microbiol 2016; 9:e35520. [PMID: 27800145 PMCID: PMC5086081 DOI: 10.5812/jjm.35520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 07/23/2016] [Accepted: 08/07/2016] [Indexed: 11/22/2022] Open
Abstract
Background Years after the development of antituberculosis (TB) drugs, many people continue to suffer from this disease. To control the spread of TB, strains of the Mycobacterium tuberculosis complex need to be determined, and sources of infection must be identified. Such steps should help to prevent transmission of the infection. Objectives The aim of this study was to perform molecular genotyping of isolates of the M. tuberculosis complex obtained from patients in northwestern Iran. Methods One hundred ninety-four culture-positive M. tuberculosis isolates obtained from patients in northwestern Iran were analyzed using the mycobacterial interspersed repetitive unit-exact tandem repeats (MIRU-ETR) method. Results The MIRU-ETR method distinguished 162 different patterns in the 194 isolates, comprising 23 clusters and 139 unique patterns. Its discriminatory power according to the Hunter-Gaston discriminatory index (HGDI) was 0.9978. The largest cluster contained six isolates. Conclusions This research indicated that various strains of M. tuberculosis were responsible for TB and that the majority of cases were due to reactivation.
Collapse
Affiliation(s)
- Mahya Pourostadi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Jalil Rashedi
- Tuberculosis and Lung Disease Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Corresponding author: Jalil Rashedi, Tuberculosis and Lung Disease Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Golgasht Ave., Azadi St., Tabriz, IR Iran. Tel: +98-4133392633, Fax: +98-4133371971, E-mail:
| | - Behroz Mahdavi Poor
- Department of Laboratory Science, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Medical Parasitology, Faculty of Medicine, Tarbiat Modares University, Tehran, IR Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Samaneh Shirazi
- Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, IR Iran
| | - Mohammad Asgharzadeh
- Hematology-Oncology Research Center, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, IR Iran
| |
Collapse
|
7
|
France AM, Grant J, Kammerer JS, Navin TR. A field-validated approach using surveillance and genotyping data to estimate tuberculosis attributable to recent transmission in the United States. Am J Epidemiol 2015; 182:799-807. [PMID: 26464470 DOI: 10.1093/aje/kwv121] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/27/2015] [Indexed: 01/20/2023] Open
Abstract
Tuberculosis genotyping data are frequently used to estimate the proportion of tuberculosis cases in a population that are attributable to recent transmission (RT). Multiple factors influence genotype-based estimates of RT and limit the comparison of estimates over time and across geographic units. Additionally, methods used for these estimates have not been validated against field-based epidemiologic assessments of RT. Here we describe a novel genotype-based approach to estimation of RT based on the identification of plausible-source cases, which facilitates systematic comparisons over time and across geographic areas. We compared this and other genotype-based RT estimation approaches with the gold standard of field-based assessment of RT based on epidemiologic investigation in Arkansas, Maryland, and Massachusetts during 1996-2000. We calculated the sensitivity and specificity of each approach for epidemiologic evidence of RT and calculated the accuracy of each approach across a range of hypothetical RT prevalence rates plausible for the United States. The sensitivity, specificity, and accuracy of genotype-based RT estimates varied by approach. At an RT prevalence of 10%, accuracy ranged from 88.5% for state-based clustering to 94.4% with our novel approach. Our novel, field-validated approach allows for systematic assessments over time and across public health jurisdictions of varying geographic size, with an established level of accuracy.
Collapse
|
8
|
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
|
9
|
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
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Nabyonga L, Kateete DP, Katabazi FA, Odong PR, Whalen CC, Dickman KR, Moses JL. Determination of circulating Mycobacterium tuberculosis strains and transmission patterns among pulmonary TB patients in Kawempe municipality, Uganda, using MIRU-VNTR. BMC Res Notes 2011; 4:280. [PMID: 21835016 PMCID: PMC3162915 DOI: 10.1186/1756-0500-4-280] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 08/11/2011] [Indexed: 11/29/2022] Open
Abstract
Background Mycobacterial interspersed repetitive units - variable number of tandem repeats (MIRU-VNTR) genotyping is a powerful tool for unraveling clonally complex Mycobacterium tuberculosis (MTB) strains and detection of transmission patterns. Using MIRU-VNTR, MTB genotypes and their transmission patterns among patients with new and active pulmonary tuberculosis (PTB) in Kawempe municipality in Kampala, Uganda was determined. Results MIRU-VNTR genotyping was performed by PCR-amplification of 15 MTB-MIRU loci from 113 cultured specimens from 113 PTB patients (one culture sample per patient). To determine lineages, the genotypes were entered into the MIRU-VNTRplus database [http://www.miru-vntrplus.org/] as numerical codes corresponding to the number of alleles at each locus. Ten different lineages were obtained: Uganda II (40% of specimens), Uganda I (14%), LAM (6%), Delhi/CAS (3%), Haarlem (3%), Beijing (3%), Cameroon (3%), EAI (2%), TUR (2%) and S (1%). Uganda I and Uganda II were the most predominant genotypes. Genotypes for 29 isolates (26%) did not match any strain in the database and were considered unique. There was high diversity of MIRU-VNTR genotypes, with a total of 94 distinct patterns. Thirty four isolates grouped into 15 distinct clusters each with two to four isolates. Eight households had similar MTB strains for both index and contact cases, indicating possible transmission. Conclusion MIRU-VNTR genotyping revealed high MTB strain diversity with low clustering in Kawempe municipality. The technique has a high discriminatory power for genotyping MTB strains in Uganda.
Collapse
Affiliation(s)
- Lydia Nabyonga
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda.
| | | | | | | | | | | | | |
Collapse
|
12
|
Reyes JF, Chan CHS, Tanaka MM. Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:811-8. [PMID: 21683165 DOI: 10.1016/j.meegid.2011.05.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 05/21/2011] [Accepted: 05/22/2011] [Indexed: 11/24/2022]
Abstract
Homoplasy is the occurrence of genotypes that are identical by state but not by descent. It arises through a number of means including convergent and reverse evolution, and horizontal gene transfer. When using molecular markers that are based on sequences possessing a finite number of character states, such as VNTR or spoligotypes, this is an unavoidable phenomenon. Here we discuss the extent of homoplasy and its impact on inferences drawn from spoligotypes and VNTR in epidemiological studies of tuberculosis. To further explore this problem, we developed a computer simulation model combining the processes of mutation and transmission. Our results show that while the extent of homoplasy is not negligible, its effect on the proportion of isolates clustered ("n-1 method") is likely to be relatively low for spoligotyping. For VNTR-typing, homoplasy occurs at a low rate provided the number of loci used is high and the mutation rate is relatively high. However, deep phylogenetic inferences using spoligotypes or VNTRs with a small number of loci are likely to be unreliable.
Collapse
Affiliation(s)
- Josephine F Reyes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | | |
Collapse
|
13
|
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
|