Genetic diversity assessment of the Mycobacterium tuberculosis isolates of patients with tuberculosis in Karaj, Iran

Abstract Background Tuberculosis (TB) is an old issue that is presently measured as a significant challenge. Molecular characterization of Mycobacterium tuberculosis has contributed to TB control. The present survey was aimed to assess the genetic diversity of M. tuberculosis strains isolated from patients with TB in Karaj, Iran. Methods Seventeen M. tuberculosis isolates from 2012 to 2013 were collected and subjected to an IS6110 restriction fragment length polymorphism (IS6110-RFLP) analysis. Demographically, 6 females and 14 males who had Iranian citizenship were included in this study. Results Sixteen different genetic types were obtained after enzymatic digestion and RFL analysis. Copy numbers of IS6110 in each isolate ranged from 0 to 12. The majority of isolates (66%) harbored copy numbers between 6 and 12. Each isolates harbored 6.9 copies of the IS6110 marker. Nine isolates harbored 10 to 12 copies of the IS6110 marker, 5 isolates harbored 6 to 10 copies, and 2 others harbored copies less than 6. No copy of IS6110 was found among the 4 isolates. No relationship was found between gender and copy numbers. Conclusions The high genetic diversity found amongst the M. tuberculosis isolates maybe show different sources of infection and the importance of reemerging of the TB. However, further surveys should perform to assess other molecular epidemiologic aspects of M. tuberculosis in Iran.

Download Full-text

Genetic diversity and drug susceptibility patterns of the Mycobacterium tuberculosis complex in Yunnan, China

Bioscience Reports ◽

10.1042/bsr20181746 ◽

2019 ◽

Vol 39 (5) ◽

Author(s):

Ruolan Bai ◽

Shuijing Chi ◽

Xiaofei Li ◽

Xiting Dai ◽

Zhenhua Ji ◽

...

Keyword(s):

Public Health ◽

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Public Health Problem ◽

Drug Susceptibility ◽

Drug Resistant ◽

Global Public Health ◽

High Genetic Diversity ◽

Dominant Feature ◽

Mdr Tb

AbstractTuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) which has been threatening global public health for many years. High genetic diversity is dominant feature of Mtb. Increasing cases of multidrug-resistant (MDR) tuberculosis (MDR-TB) is a serious public health problem to TB control in China. Spontaneous mutations in the Mtb genome can alter proteins which are the target of drugs, making the bacteria drug resistant. The purpose of the present study was to analyze the genotype of Mtb isolates from some areas in Yunnan, China and explore the association between genotypes and MDR-TB. Using spoligotyping, we identified Beijing genotypes, six non-Beijing genotypes and a number of orphan genotypes from 270 Mtb isolates from patients in Yunnan Province during 2014–2016. Of 270 Mtb isolates, 102 clinical Mtb strains were identified as drug-resistant (DR) by drug susceptibility testing (DST), among them, 52 MDR strains. Beijing genotypes occupied the highest MDR proportion (78.85%) followed by the orphan genotypes (15.38%). The characteristics of MDR strains showed high genetic diversity. The results will help to efficiently improve diagnosis and treatment and provide valuable information for Mtb molecular epidemiology.

Download Full-text

Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers

Czech Journal of Genetics and Plant Breeding ◽

10.17221/220/2013-cjgpb ◽

2014 ◽

Vol 50 (No. 3) ◽

pp. 216-225 ◽

Cited By ~ 3

Author(s):

L. Havlíčková ◽

E. Jozová ◽

A. Rychlá ◽

M. Klíma ◽

V. Kučera ◽

...

Keyword(s):

Genetic Diversity ◽

Brassica Napus ◽

Oilseed Rape ◽

Issr Markers ◽

Appropriate Technology ◽

Winter Oilseed Rape ◽

Brassica Napus L ◽

High Genetic Diversity ◽

Diversity Assessment ◽

Breeding Programmes

The genetic diversity of 94 accessions of winter oilseed rape (Brassica napus L.), representing past and contemporary material utilized in the Czech breeding programmes, was determined using microsatellites (SSRs), ISSRs and AFLPs. All three kinds of markers differed in the range of observed polymorphism and differentiated clearly each accession. Altogether 89 SSR, 1003 AFLP and 53 ISSR markers were evaluated. Their average rates of polymorphic bands were 100%, 53.9% and 90.6%, respectively, indicating high genetic diversity among the accessions. The greatest genetic distance was found by ISSRs (62.3%) whereas significantly lower distances of 49.4% in SSRs and 35.5% in AFLPs were observed. The genetic similarity matrix clearly distinguished all accessions. A set of the most distinct varieties was established. The analysis of the genetic pattern of the accessions indicated two groups comprising most of the modern Czech breeding materials, revealing a distinct shift in breeding. Surprisingly, molecular analyses did not support  breeders’ views about a narrow genetic base of the Czech breeding materials. The choice of appropriate technology for different aspects of germplasm evaluation is also discussed.

Download Full-text

High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone

BMC Microbiology ◽

10.1186/1471-2180-8-103 ◽

2008 ◽

Vol 8 (1) ◽

pp. 103 ◽

Cited By ~ 40

Author(s):

Susanne Homolka ◽

Erik Post ◽

Barbara Oberhauser ◽

Abu George ◽

Lars Westman ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Sierra Leone ◽

Mycobacterium Tuberculosis Complex ◽

Tuberculosis Complex ◽

High Genetic Diversity

Download Full-text

Genetic diversity ofFrankiastrains in root nodules fromHippophae¨ rhamnoidesL.

Botany ◽

10.1139/b07-133 ◽

2008 ◽

Vol 86 (3) ◽

pp. 240-247 ◽

Cited By ~ 1

Author(s):

Li-hong Chen ◽

Jian Liu ◽

Gui-min Yao ◽

Wei Yan

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Restriction Analysis ◽

Root Nodules ◽

Plant Cover ◽

Practical Importance ◽

Intergenic Spacer ◽

Rflp Analysis ◽

Northern China ◽

High Genetic Diversity

The Hippophae¨ rhamnoides L. – Frankia symbiosis is of ecological and practical importance, but very little is known about H. rhamnoides-infective Frankia strains. To address this problem, we have used PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of nifD–nifK intergenic spacer (IGS) to estimate their genetic diversity at 19 sites in Northern China. Restriction analysis indicated that H. rhamnoides-infective Frankia had a high genetic diversity; the samples were divided into nine RFLP patterns (A–I). Elevation and precipitation likely affect the distribution of different Frankia patterns in root nodules. The patterns A and D were present in relatively large areas, which were located at various elevations; however, the distribution of patterns B, C, E, F, G, H, and I generally followed a geographic range. The richness of Frankia diversity was influenced by plant cover and geographic factors such as elevation and precipitation. H. rhamnoides cover had a higher diversity than that of natural vegetation cover. The center part of the geographical range, with intermediate elevation and precipitation, had a higher level of Frankia diversity than that of the west part and east part with high or low elevations and precipitations, respectively. The nifD–nifK IGS regions were sequenced from 28 nodule samples. Phylogenetic analysis showed that H. rhamnoides-infective Frankia strains were all clustered with the Elaeagnus group, and the diversity of this group was quite extensive. Phylogenetic relationships between Hippophae¨ and Elaeagnus-infective Frankia strains were relatively close to each other. Although not very close to either Hippophae¨- or Elaeagnus-infective Frankia strains, Shepherdia -infective strain SCN10a was closer to Hippophae¨-infective strains than to Elaeagnus- infective strains. This is the first detailed report on the genetic diversity and phylogenetic analysis of H. rhamnoides-infective Frankia.

Download Full-text

Phylogenetic analysis and genetic diversity of Phytophthora palmivora causing black pod disease of cocoa in Malaysia.

Plant Health Progress ◽

10.1094/php-02-21-0030-fi ◽

2021 ◽

Author(s):

Wael Alsultan ◽

Ganesan Vadamalai ◽

Halimi Mohd Saud ◽

Ahmad Khairulmazmi ◽

Mui Yun Wong ◽

...

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Phylogenetic Analyses ◽

Inter Simple Sequence Repeat ◽

Its Rdna ◽

Phytophthora Palmivora ◽

High Genetic Diversity ◽

Study Results ◽

Black Pod ◽

Black Pod Disease

Black pod, caused by Phytophthora spp., occurs worldwide and is a major problem to cocoa farmers in Malaysia. Limited studies addressed causal agents of black pod disease of cocoa in Malaysia as well as their genetic diversity. Therefore, this study was initiated to isolate and identify Phytophthora from the main cocoa plantations infected by black pod in Malaysia using sequence analyses of the ITS rDNA, EF-1α, and COX I gene regions. A total of 36 Phytophthora isolates were obtained from infected cocoa plantations from five states of Malaysia in 2016 and 14 isolates in 2013. Six Phytophthora isolates obtained from durian crop in 2013 were also used in this study. Results of phylogenetic analyses of combined dataset of the ITS rDNA, COX I and EF-1α confirmed that all Phytophthora isolates belonged to P. palmivora. P. palmivora isolates obtained from cocoa and durian clustered into different subclades based on the three regions examined. The study also examined the genetic diversity within a population of 56 P. palmivora isolates using random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers. The results of both markers indicated relatively high diversity among P. palmivora isolates. The complete separation was based on host and year of isolation. The study suggests that one species of Phytophthora viz. P. palmivora, is responsible for black pod of cocoa in Malaysia. However, the relatively high genetic diversity and separation of isolates into different clades may suggest that P. palmivora has been introduced into Malaysia via different sources.

Download Full-text

Predominance of Central Asian strain (ST 26) in Mycobacterium tuberculosis isolates from Balochistan by spoligotyping

The Journal of Infection in Developing Countries ◽

10.3855/jidc.10803 ◽

2019 ◽

Vol 13 (07) ◽

pp. 619-625

Author(s):

Muhammad Shafee ◽

Ferhat Abbas ◽

Zunera Tanveer ◽

Andrew Whitelaw ◽

Lemese Ah Tow ◽

...

Keyword(s):

Public Health ◽

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Latin American ◽

Base Line ◽

East African ◽

High Genetic Diversity ◽

Asian Strain ◽

Central Asian ◽

Insight Into

Introduction: Tuberculosis is a chronic debilitating infectious disease causing a severe challenge to public health, especially in developing countries. The aim of this study was to examine genetic diversity in Mycobacterium tuberculosis strains circulating in the Balochistan region of Pakistan. Methodology: One hundred isolates collected from patients visiting the Fatima Jinnah TB Hospital in Quetta were subjected to genotype analysis by spoligotyping. Results: Three main genotypes were identified: Central Asian Strain 1 (CAS1) (n = 89), East African Indian (EAI) strain (n = 7) and Latin American Mediterranean (LAM) strain (n = 3). The CAS1 clade (ST 26) had high genetic diversity represented by seven different spoligopatterns, of which one had major predominace (n = 75). Conclusions: This is the first insight into the genotype of M. tuberculosis strains in the Balochistan region that might serve as a base line study for control of tuberculosis in the community.

Download Full-text

Genetic variability in multidrug-resistant Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in North India

BMC Microbiology ◽

10.1186/s12866-021-02174-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ajay Vir Singh ◽

Suman Singh ◽

Anjali Yadav ◽

Shweta Kushwah ◽

Rajbala Yadav ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Genetic Variability ◽

Pulmonary Tuberculosis ◽

Control Strategies ◽

Multidrug Resistant ◽

North India ◽

Drug Resistant ◽

High Genetic Diversity ◽

Mdr Tb

Abstract Background Information on the genetic variability of drug resistant isolates of Mycobacterium tuberculosis is of paramount importance to understand transmission dynamics of disease and to improve TB control strategies. Despite of largest number of multidrug-resistant (MDR) tuberculosis cases (1, 30,000; 27% of the global burden), strains responsible for the expansion or development of drug-resistant Mycobacterium tuberculosis infections have been poorly characterized in India. Present study was aimed to investigate the genetic diversity in MDR isolates of Mycobacterium tuberculosis in North India. Results Spacer oligonucleotide typing (spoligotyping) was performed on 293 clinical MDR isolates of Mycobacterium tuberculosis recovered from cases of pulmonary tuberculosis from North India. Spoligotyping identified 74 distinct spoligotype patterns. Comparison with an international spoligotype database (spoldb4 database) showed that 240 (81.91%) and 32 (10.92%) strains displayed known and shared type patterns, while 21 (7.16%) strains displayed unique spoligotype patterns. Among the phylogeographic lineages, lineage 3 (East African-Indian) was found most predominant lineage (n = 159, 66.25%), followed by lineage 2 (East Asian; n = 34, 14.16%), lineage 1 (Indo-Oceanic; n = 30, 12.50%) and lineage 4 (Euro American; n = 17, 7.08%). Overall, CAS1_DEL (60.41%; SITs 2585, 26, 2694, 309, 381, 428, 1401, 141, 25, 1327) was found most pre-dominant spoligotype pattern followed by Beijing (14.16%; SITs255, 260, 1941, 269) and EAI3_IND (5.00%; SITs 298, 338, 11). The demographic and clinical characteristics were not found significantly associated with genotypic lineages of MDR-M.tuberculosis isolates recovered from pulmonary TB patients of North India. Conclusions Present study reveals high genetic diversity among the Mycobacterium tuberculosis isolates and highlights that SIT141/CAS1_Del followed by SIT26/ Beijing lineage is the most common spoligotype responsible for the development and transmission of MDR-TB in North India. The high presence of shared type and unique spoligotype patterns of MDR strains indicates epidemiological significance of locally evolved strains in ongoing transmission of MDR-TB within this community which needs to be further monitored using robust molecular tools with high discriminatory power.

Download Full-text

Establishment and confirmation of heterotic groups and genetic diversity assessment of maize inbred lines using microsatellite data

Genetika ◽

10.2298/gensr1603067n ◽

2016 ◽

Vol 48 (3) ◽

pp. 1067-1076

Author(s):

Ana Nikolic ◽

Jelena Bogosavljevic ◽

Zoran Camdzija ◽

Milomir Filipovic ◽

Dragan Kovacevic ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Field Testing ◽

Pedigree Data ◽

High Genetic Diversity ◽

Heterotic Groups ◽

Mean Values ◽

Average Value ◽

Diversity Assessment ◽

Maize Inbreds

Twenty-seven maize inbreds (12 commercial and 15 developing lines) from Maize Research Institute breeding program were subjected to microsatelite analysis. The aim was genetic diversity determination, establishing relationships among tested lines and assigning them to heterotic groups according to molecular marker data. Number of alelles detected was 97, with an average of 3.23. Major allele frequency was in a range from 0.33 to 0.82 (average 0.55). The highest value for observed heterozygosity was 10% for several developing lines. Mean values for gene diversity and PIC were 0.56 and 0.48, respectively. Frequency-based distances were calculated using Roger?s coefficient and average value of 0.57 indicates high genetic diversity in analyzed maize inbreds. Distance matrices were subjected to cluster analysis and PCA. Multivariate analysis methods showed considerable concurrency with pedigree data. Results of analysis with 30 microsatellite markers could be useful for defining/redefining heterotic groups but should be complemented with field testing data.

Download Full-text

Diversity assessment among native Middle Egypt rabbit populations in North Upper-Egypt province by microsatellite polymorphism

World Rabbit Science ◽

10.4995/wrs.2017.5298 ◽

2017 ◽

Vol 25 (1) ◽

pp. 9 ◽

Cited By ~ 2

Author(s):

A.M. Emam ◽

A.A.A. Azoz ◽

G.M.K. Mehaisen ◽

N. Ferrand ◽

N.A. Ahmed

Keyword(s):

Genetic Diversity ◽

Developed Countries ◽

Microsatellite Polymorphism ◽

Factorial Correspondence Analysis ◽

Statistical Parameters ◽

High Genetic Diversity ◽

Upper Egypt ◽

Mean Values ◽

Diversity Assessment ◽

The Mean

<p>Safeguarding biodiversity is an important goal for animal production in developed countries. This study investigated genetic diversity among native Middle-Egypt rabbit (NMER) populations in North Upper-Egypt province by using microsatellite polymorphism. Nineteen microsatellite loci were used in the study and an area of 231 km was surveyed, as native rabbits covered 14 points belonging to four Northern Upper Egypt governorates (South Giza, Fayoum, Beni Suef and Minya). Standard statistical parameters of genetic variability within and between populations confirmed that the highest genetic diversity was found towards the south. Among NMER populations, the mean number of alleles per locus was lowest in South Giza (5.32), while it was highest in Minya (6.00). This study found that NMER featured a high number of private alleles ranging between 7 and 11 (mean value was 10.5). Results also showed a high genetic diversity in NMER populations and that heterozygosity ranged between 0.384 and 0.445, strongly indicating extensive genetic variation in the NMER populations. The mean values of observed and expected heterozygosity were 0.405 and 0.612, respectively. Factorial correspondence analysis and neighbour joining trees (NJ) showed 2 main NMER rabbit groups: the Northern group (South Giza and Fayoum) and the Southern group (Beni Suef and Minya). All populations showed a high percentage of assignment in this study (0.913 to 0.946). The structure analysis showed that each population existed in separate clusters. This research provides an overview of genetic diversity of NMER populations in the Northern Upper Egypt province for the first time. In conclusion, results of this study could be used to designate priorities for conservation of NMER populations.</p>

Download Full-text