Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage of<i>Mycobacterium tuberculosis</i>in Israel Originating Predominantly in Sub-Saharan Africa

Freidlin, Paul J.; Goldblatt, Drora; Kaidar-Shwartz, Hasia; Rorman, Efrat

doi:10.1128/jcm.01270-09

Cited by 11 publications

(17 citation statements)

References 80 publications

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“…Of all the Israeliborn patients, none recalled having had contact with a known TB patient; 15 could recall close contact with a non-Israeli-born citizen, but not with a non- Our results suggest that the CAS family constitutes the predominant family of M. tuberculosis strains among migrants from EES, while the most significant spoligotype pattern was the CAS1_Delhi SIT 25, which was previously designated as PETRA in Israel. 12 These findings are in agreement with another publication 13 that reported that the CAS1_Delhi family (SIT25) was shared by 35% of strains in Sudan. The predominance of the Delhi/CAS lineage was also described in north-west Ethiopia, 14 where M. tuberculosis Delhi/CAS accounts for 39% of the strains investigated.…”

Section: Cluster Analysissupporting

confidence: 91%

“…Most of the patients infected with the CAS strains originated from EES (73%); only 4% originated from FSU countries ( Table 1). Of the CAS family, CAS1_Delhi SIT 25, known in our laboratory as PETRA (polymorphic exact tandem repeat A), 12 predominated (46%), with 89% originating from EES (data not shown). The T-clade was found to be more heterogeneous, with isolates from patients arriving from both FSU (33%) and EES (38%).…”

Section: Molecular Epidemiology Mappingmentioning

confidence: 89%

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Molecular epidemiology and mapping of tuberculosis in Israel: do migrants transmit the disease to locals?

Goldblatt

Rorman

Chemtob³

et al. 2014

int j tuberc lung dis

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Section: Cluster Analysissupporting

confidence: 91%

Section: Molecular Epidemiology Mappingmentioning

confidence: 89%

Molecular epidemiology and mapping of tuberculosis in Israel: do migrants transmit the disease to locals?

Goldblatt

Rorman

Chemtob³

et al. 2014

int j tuberc lung dis

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“…BioNumerics version 3.5 (Applied Maths, Belgium) was used under default settings [15] to construct a minimum spanning tree (MST, Figure 1) from the restriction site data (Table S3) on Mycobacterium species and control species from 3 related mycolic acid-containing genera. M. tuberculosis complex species were given one entry due to identical restriction sites on the given species, and likewise for M. goodie and M. wolinskyi which had identical restriction sites.…”

Section: Population Structure Analysismentioning

confidence: 99%

“…Diagnoses of non-tuberculous Mycobacterium (NTM) associated diseases have been increasing [4][5][6]. Therapeutic modalities for the treatment of Mycobacterium-associated diseases are constantly being challenged by the development of multiple drug resistance [7][8][9][10] and in particular for Mycobacterium tuberculosis, the ability to evade (avoid or subvert) various components of the immune system [11][12][13][14][15][16][17][18]. The discovery of new therapeutics and vaccines is of paramount importance, but is dependent on deeper understanding of the structural and functional nature of the molecular biology of Mycobacterium species [19].…”

Section: Introductionmentioning

confidence: 99%

A New Paradigm for Genus Mycobacterium Population Structure

Freidlin¹

2013

J Bacteriol Parasitol

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The genus Mycobacterium contains the pathogenic species tuberculosis and leprae, and additionally at least 148 sometimes opportunistic pathogenic species that occupy environmental niches. The genus Mycobacterium is in the order Actinomycetes along with other acid-fast genera with mycolic acids in their cell walls, such as Corynebacterium, Nocardia, and Rhodococcus. The DNA-dependent RNA polymerase subunit b gene rpoB, is relatively conserved among these bacteria. Sequence polymorphism in a 342bp fragment of rpoB is sufficient to differentiate among most species of Mycobacterium. However, construction of a robust and testable phylogeny or population structure based on this polymorphism, or polymorphism in other genomic regions, has remained elusive. This study presents a new paradigm for the resolution of genus Mycobacterium population structure. A minimum spanning tree (MST) was constructed on restriction enzyme site polymorphisms detected in silico for 5 enzymes, on the 342bp rpoB fragment obtained from GenBank data for 47 Mycobacterium species, and one species each from Corynebacterium, Nocardia and Rhodococcus. The MST was empirically divided into 3 regions. All the rapidly growing mycobacteria (RGM), with a halo of slowly growing mycobacteria (SGM), were found in MST-region 1. The correctness of the MST-regions model of genus Mycobacterium population structure was validated by statistically confirmed linkage disequilibrium of certain restriction site alleles. For certain alleles, SGM in MST-region 1 resembled the RGM of MST-region 1 more than the SGM of MST-region 3. The model provided a framework consistent with published genotypic and phenotypic observations, including expectations from comparative genomics and ribosomal RNA (rRNA) gene properties' distribution among species, and reported cladistic groupings of species. Corynebacterium diphtheriae, Nocardia nova and Rhodococcus equi belonged to MSTregions 2, 3, and 1 respectively. In conclusion, the MST-regions model of genus Mycobacterium population structure was robust, unambiguous, transparent for alleles, consistent with genotypes and phenotypes, and statistically testable.

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“…A high agreement (99.2%) was found between the results of Hitachi i-chips and that of the QIAxcel CE system. Freidlin et al [40] applied MIRU-VNTR-CE typing to find the origin of the new tuberculosis cases in Israel. They discovered that the polymorphic exact tandem repeat A (PETRA) lineage is large and a main contribution to the new cases of tuberculosis.…”

Section: Detecting and Diagnosing Bacteriamentioning

confidence: 99%

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Lian

Zhao

2016

Clinical Chemistry and Laboratory Medicine (CCLM)

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Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

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Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage ofMycobacterium tuberculosisin Israel Originating Predominantly in Sub-Saharan Africa

Cited by 11 publications

References 80 publications

Molecular epidemiology and mapping of tuberculosis in Israel: do migrants transmit the disease to locals?

Molecular epidemiology and mapping of tuberculosis in Israel: do migrants transmit the disease to locals?

A New Paradigm for Genus Mycobacterium Population Structure

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

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