Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

Couvin, David; Rastogi, Nalin

doi:10.1016/j.tube.2015.02.023

Cited by 52 publications

(53 citation statements)

References 45 publications

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“…This suggests that while most of the MDR strains could have developed drug resistance within Gabon, the SIT1 strains and the SIT260 strain may have been MDR when they were introduced into Libreville. The origin of these strains is a mystery, since reports from neighboring countries suggest that Beijing strains are not common in the region, and those found were generally not MDR (27–29). Follow-up studies are in progress to determine the extent and epidemiology of the apparent SIT1 MDR outbreak strain and to see if the MDR, FQ r , SM r SIT260 Beijing strain is also spreading.…”

Section: Discussionmentioning

confidence: 99%

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon

et al. 2017

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Multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis pose major problems for global health. The GeneXpert MTB/RIF (Xpert) assay rapidly detects resistance to rifampin (RIFr), but for detection of the additional resistance that defines MDR-TB (MDR tuberculosis) and XDR-TB, and for molecular epidemiology, specimen cultures and a biosafe infrastructure are generally required. We sought to determine whether the remnants of sputa prepared for the Xpert assay could be used directly to find mutations associated with drug resistance and to study molecular epidemiology, thus providing precise characterization of MDR-TB cases in countries lacking biosafety level 3 (BSL3) facilities for M. tuberculosis cultures. After sputa were processed and run on the Xpert instrument, the leftovers of the samples prepared for the Xpert assay were used for PCR amplification and sequencing or for a line probe assay to detect mutations associated with resistance to additional drugs, as well as for molecular epidemiology with spoligotyping and selective mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing. Of 130 sputum samples from Gabon tested with the Xpert assay, 124 yielded interpretable results; 21 (17%) of these were determined to be RIFr. Amplification and sequencing or a line probe assay of the Xpert remnants confirmed 18/21 samples as MDR, corresponding to 12/116 (9.5%) new and 6/8 (75%) previously treated TB patients. Spoligotyping and MIRU typing with hypervariable loci identified an MDR Beijing strain present in five samples. We conclude that the remnants of samples processed for the Xpert assay can be used in PCRs to find mutations associated with the resistance to the additional drugs that defines MDR and XDR-TB and to study molecular epidemiology without the need for culturing or a biosafe infrastructure.

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Section: Discussionmentioning

confidence: 99%

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon

et al. 2017

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“…Thus, drug resistance was significantly linked to Beijing strains in Russia, Southern Asia, Southeast Asia, and European countries but not to those in the Americas, Western Asia, China, and Japan. Furthermore, global data in the SITVIT2 database show that the SIT190/ Beijing pattern, a rare but emerging spoligotype pattern, was significantly more associated with MDR TB than was the traditional SIT1/Beijing pattern (P Ͻ 0.0001) (596). Finally, regarding information provided by bioinformatic tools and online georeferencing using Google API, a recent study was conducted in Baghdad, Iraq (597), where spoligoforest analysis showed that the bulk of TB isolates in postwar Iraq is limited to two phylogenetically related groups of MTBC strains belonging to the T and CAS lineages (SIT1144/T1 and SIT309/CAS1-Delhi), while georeferencing highlighted statistically significant differences between isolates from Baghdad and those from other cities in Iraq, regarding both demographic and drug resistance information.…”

Section: Examples Of Recent Studies Using the Sitvit2 Databasementioning

confidence: 99%

“…Findings from recent studies showing an association between phylogenetic lineages and demographic and epidemiological parameters using the SITVIT2 database include (i) the finding of high phylogeographical specificity of M. africanum for Western Africa, with Guinea-Bissau being the epicenter (591); (ii) evidence that the TB epidemic in Sweden a century ago was caused by a closely knit pool of evolutionarily recent strains restricted to Sweden and its immediate neighbors (592); (iii) evidence for a prolonged, clonal, hospital-based outbreak of MDR TB among HIV-positive patients in Peru (593); (iv) determination of the predominance of the Euro-American family among elderly TB patients in Finland just as in Sweden, with the main difference being the presence of significant proportions of isolates of the Ural lineage among Finnish-born cases (also found in Russia, Latvia, and Estonia) but not in Sweden (594); and (v) determination of the association of the Beijing lineage with excessive drug resistance, including MDR and/or XDR TB (286,502,595), and the finding that even though the proportion of drug-resistant strains is significantly higher for Beijing than for non-Beijing strains globally, there are important variations in the distribution of drug resistance (596). Thus, drug resistance was significantly linked to Beijing strains in Russia, Southern Asia, Southeast Asia, and European countries but not to those in the Americas, Western Asia, China, and Japan.…”

Section: Examples Of Recent Studies Using the Sitvit2 Databasementioning

confidence: 99%

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

et al. 2016

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SUMMARYMolecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods forMycobacterium tuberculosisand nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

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“…Beijing lineage of Mycobacterium tuberculosis complex (MTBC) which belongs to the lineage 2 (East-Asian) as defined by Regions of Differences-Large Sequence Polymorphisms (RD-LSPs), constitutes the most predominant lineage in East Asia 2–4 . Partially attributed to its properties of hypervirulence, multi drug-resistance (MDR), and association with cases of mixed infections 5–8 , it has today spread worldwide 9–11 , leading to much effort to monitor its epidemiology within a broadened concept of its evolutionary genetics. In this context, we decided to perform a detailed mapping of available genotyping data on Beijing lineage strains in mainland China and Taiwan by means of phylogenetic and Bayesian population structure analyses to delineate tentative Beijing clonal complexes with distinct genetic and phylogeographical characteristics.…”

Section: Introductionmentioning

confidence: 99%

New Mycobacterium tuberculosis Beijing clonal complexes in China revealed by phylogenetic and Bayesian population structure analyses of 24-loci MIRU-VNTRs

Zheng

Reynaud

Zhao

et al. 2017

Sci Rep

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Beijing lineage of Mycobacterium tuberculosis constitutes the most predominant lineage in East Asia. Beijing epidemiology, evolutionary history, genetics are studied in details for years revealing probable origin from China followed by worldwide expansion, partially linked to higher mutation rate, hypervirulence, drug-resistance, and association with cases of mixed infections. Considering huge amount of data available for 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats, we performed detailed phylogenetic and Bayesian population structure analyses of Beijing lineage strains in mainland China and Taiwan using available 24-loci MIRU-VNTR data extracted from publications or the SITVIT2 database (n = 1490). Results on genetic structuration were compared to previously published data. A total of three new Beijing clonal complexes tentatively named BSP1, BPS2 and BSP3 were revealed with surprising phylogeographical specificities to previously unstudied regions in Sichuan, Chongqing and Taiwan, proving the need for continued investigations with extended datasets. Such geographical restriction could correspond to local adaptation of these “ecological specialist” Beijing isolates to local human host populations in contrast with “generalist pathogens” able to adapt to several human populations and to spread worldwide.

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Tuberculosis – A global emergency: Tools and methods to monitor, understand, and control the epidemic with specific example of the Beijing lineage

Cited by 52 publications

References 45 publications

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

New Mycobacterium tuberculosis Beijing clonal complexes in China revealed by phylogenetic and Bayesian population structure analyses of 24-loci MIRU-VNTRs

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