Genotyping of
            <i>Mycobacterium Tuberculosis</i>
            : Application in Epidemiologic Studies

Kato‐Maeda, Midori; Metcalfe, John; Flores, Laura L

doi:10.2217/fmb.10.165

Cited by 104 publications

(102 citation statements)

References 112 publications

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“…Basic strain classification in phylogenetic families was performed using the MIRU-VNTRplus server (22,33). To determine the spoligotype family (26), patterns were compared with those in the international database of spoligotyping patterns (http://www.miru -vntrplus.org/MIRU/index.faces) and the rules for the spoligotype family prototype (16). MIRU-VNTR profiles with double alleles at a single locus were considered to represent heterogeneous populations of the same strain, whereas those with double alleles at 2 or more loci were considered to represent mixed infections or to indicate cross-contamination (34,35).…”

Section: Methodsmentioning

confidence: 99%

“…This paradox of improved TB management and worsening resistance prevalence has been explained by increases in the notified cases, i.e., in case detection, although treatment outcomes remain poor (12). Basically, the observed increases in MDR-TB rates may result from two factors, i.e., transmission of MDR-TB and acquired resistance due to ineffective TB treatment selecting for spontaneous mutations in specific genes associated with drug resistance (13,14).Molecular strain typing (genotyping) has significantly contributed worldwide to the understanding of TB epidemiology and transmission dynamics (15,16), by confirming outbreaks (17) and identifying the clonal spread of successful strains, including MDR strains (18,19). Furthermore, molecular typing has shown that the Mycobacterium tuberculosis complex (MTBc) has a diverse population structure, being composed of seven lineages of human …”

mentioning

confidence: 99%

“…Molecular strain typing (genotyping) has significantly contributed worldwide to the understanding of TB epidemiology and transmission dynamics (15,16), by confirming outbreaks (17) and identifying the clonal spread of successful strains, including MDR strains (18,19). Furthermore, molecular typing has shown that the Mycobacterium tuberculosis complex (MTBc) has a diverse population structure, being composed of seven lineages of human importance, subdivided into families (20,21) that differ not only in their geographical occurrence but also in their drug resistance profiles (19,22).…”

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confidence: 99%

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Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru

et al. 2015

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T uberculosis (TB) is among the top 10 causes of death in the global ranking (1). Although Peru accounts for only 3% of the population of the Americas, it has 9.5% of the region's TB cases. According to the World Health Organization (WHO), 21,916 new cases of pulmonary TB were reported in Peru between January and November 2013 (2). Urban areas are more affected, with 59% of all Peruvian TB cases, 82% of multidrug-resistant (MDR) TB cases, and 93% of extensively drug-resistant (XDR) TB cases occurring in Lima. Within the capital area, TB cases are heterogeneously distributed. The most affected districts are located in the northeast and together represent 86% of the reported cases in the capital (3, 4). San Juan de Lurigancho is the most populated district in this area, with 1,004,339 inhabitants (5), and reports a pulmonary TB incidence rate of 193 cases per 100,000 inhabitants, a smear-positive TB incidence rate of 126 cases per 100,000 inhabitants (6), and an overall MDR prevalence of 7% (7), exceeding the national averages for the three indicators of 103 cases per 100,000 inhabitants, 62 cases per 100,000 inhabitants, and 5.3%, respectively (8). The HIV prevalence among TB patients in this setting is similar to the national prevalence, which in 2008 was 2.6% (9).Peru has been considered a good example of the beneficial effects of implementing directly observed therapy short course (DOTS) in a country's health system (10). Nevertheless, national surveys from 1996 and 2006 have shown increases in MDR rates from 2.4% to 5.3% among new cases and from 15.7% to 23.6% among previously treated cases (11). This paradox of improved TB management and worsening resistance prevalence has been explained by increases in the notified cases, i.e., in case detection, although treatment outcomes remain poor (12). Basically, the observed increases in MDR-TB rates may result from two factors, i.e., transmission of MDR-TB and acquired resistance due to ineffective TB treatment selecting for spontaneous mutations in specific genes associated with drug resistance (13,14).Molecular strain typing (genotyping) has significantly contributed worldwide to the understanding of TB epidemiology and transmission dynamics (15,16), by confirming outbreaks (17) and identifying the clonal spread of successful strains, including MDR strains (18,19). Furthermore, molecular typing has shown that the Mycobacterium tuberculosis complex (MTBc) has a diverse population structure, being composed of seven lineages of human

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru

et al. 2015

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“…MTBC isolates representing at least 28 different spoligotypes were selected based on spoligotyping information provided by the Genotyping Laboratory of the California Department of Health Services (27,28). Spoligotyping was also used to discriminate M. bovis and M. africanum from other MTBC strains.…”

Section: Methodsmentioning

confidence: 99%

Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing

et al. 2012

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Tuberculosis (TB) remains a significant global health problem for which rapid diagnosis is critical to both treatment and control. This report describes a multiplex PCR method, the Mycobacterial IDentification and Drug Resistance Screen (MID-DRS) assay, which allows identification of members of the Mycobacterium tuberculosis complex (MTBC) and the simultaneous amplification of targets for sequencing-based drug resistance screening of rifampin-resistant (rifampin r ), isoniazid r , and pyrazinamide r TB. Additionally, the same multiplex reaction amplifies a specific 16S rRNA gene target for rapid identification of M. avium complex (MAC) and a region of the heat shock protein 65 gene (hsp65) for further DNA sequencing-based confirmation or identification of other mycobacterial species. Comparison of preliminary results generated with MID-DRS versus culturebased methods for a total of 188 bacterial isolates demonstrated MID-DRS sensitivity and specificity as 100% and 96.8% for MTBC identification; 100% and 98.3% for MAC identification; 97.4% and 98.7% for rifampin r TB identification; 60.6% and 100% for isoniazid r TB identification; and 75.0% and 98.1% for pyrazinamide r TB identification. The performance of the MID-DRS was also tested on acid-fast-bacterium (AFB)-positive clinical specimens, resulting in sensitivity and specificity of 100% and 78.6% for detection of MTBC and 100% and 97.8% for detection of MAC. In conclusion, use of the MID-DRS reduces the time necessary for initial identification and drug resistance screening of TB specimens to as little as 2 days. Since all targets needed for completing the assay are included in a single PCR amplification step, assay costs, preparation time, and risks due to user errors are also reduced.T he diagnosis and control of tuberculosis (TB) is a very significant problem in global health. A recent report by the World Health Organization (WHO) estimates that Mycobacterium tuberculosis, the causative agent of the disease, has infected one-third of the world's population (71). TB can persist in a latent state within infected individuals for decades (69). Progression to active disease occurs in approximately 5% to 10% of immunocompetent individuals and triggers the frequent cough that enables the organism to be transmitted (11). Moreover, effective treatment of patients with active TB has become more difficult with the increasing prevalence of multidrug-resistant (MDR) strains (7, 70). MDR-TB is resistant to both of the first-line drugs rifampin (RIF) and isoniazid (INH) (8). MDR-TB cases have been estimated to account for one in four new TB cases in some parts of the world (70). In the United States, MDR-TB cases comprise approximately 1.1% of new TB cases, with the majority of these cases imported from regions where the disease is endemic.All members of the M. tuberculosis complex (MTBC) are capable of causing pulmonary disease, and early diagnosis is the most effective means of TB control. Culture-based identification remains the gold standard method for TB diagnosis (1...

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“…7 Mycobacterium tuberculosis genotyping has proven to be the most important laboratory tool in understanding TB transmission. 8 In addition to studies on patient contacts; information on molecular epidemiology is useful for evaluating TB control program results. Genotyping also assists in monitoring molecular markers associated with virulence, immunogenicity, and drug resistance 9 ; among the genotyping tools available, the IS6110-restriction fragment length polymorphism (RFLP) reference standard method is based on the number of repetitions of the IS6110 sequence along the M. tuberculosis genome.…”

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confidence: 99%

Mycobacterium tuberculosis Isolates from Single Outpatient Clinic in Panama City Exhibit Wide Genetic Diversity

Sambrano

Corrêa

Almengor

et al. 2014

The American Society of Tropical Medicine and Hygiene

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Abstract. Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.Tuberculosis (TB) affects nearly 8.7 million people worldwide.1 In 2011, most TB cases were reported in Asia (59%) and Africa (26%), although cases were reported to a lesser extent in the Eastern Mediterranean Region (7.7%), the European Region (4.3%), and the Americas Region (3%). Panama stands as the country with the highest TB mortality rate in Central America.2 In 2012, more than 1,500 TB cases were reported in Panama, for an average incidence rate of 43.1 cases per 100,000 inhabitants.3 Areas located at the Pacific and Atlantic entries of the Panama Canal have harbored the highest numbers of TB cases since the Canal's construction. 4 Despite sanitation improvements in terminal port cities, recent studies have revealed elevated TB transmission as a result of a high clustering rate among multidrug-resistant TB cases. 5,6 However, data on the transmission of drug-susceptible TB within the general population remain scarce and have not been updated to reflect a second wave of immigration connected with Panama Canal expansion activities. 7Mycobacterium tuberculosis genotyping has proven to be the most important laboratory tool in understanding TB transmission. 8 In addition to studies on patient contacts; information on molecular epidemiology is useful for evaluating TB control program results. Genotyping also assists in monitoring molecular markers associated with virulence, immunogenicity, and drug resistance 9 ; among the genotyping tools available, the IS6110-restriction fragment length polymorphism (RFLP) reference standard method is based on the number of repetitions of the IS6110 sequence along the M. tuberculosis genome. 10This tool discriminates between clonally related and unrelated isolates. On the other hand, Spoligotyping focuses on detecting 43 spacer sequences in the direct repeat region of the M. tuberculosis genome. Unfortunately, the IS6110-RFLP method is a complex and laborious procedure, whereas Spoligotyping is faster and simpler but less discriminating.11,12 ...

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Genotyping of Mycobacterium Tuberculosis : Application in Epidemiologic Studies

Cited by 104 publications

References 112 publications

Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru

Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru

Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing

Mycobacterium tuberculosis Isolates from Single Outpatient Clinic in Panama City Exhibit Wide Genetic Diversity

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