Characterization of Mycobacterium tuberculosis complex isolated from iranian and afghani patients by spoligotyping method

Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis

Background

Acquiring comprehensive insight into the dynamics of Mycobacterium tuberculosis (Mtb) population structure is an essential step to adopt effective tuberculosis (TB) control strategies and improve therapeutic methods and vaccines. Accordingly, we performed this systematic review and meta-analysis to determine the overall prevalence of Mtb genotypes/ sublineages in Iran.

Methods

We carried out a comprehensive literature search using the international databases of MEDLINE and Scopus as well as Iranian databases. Articles published until April 2020 were selected based on the PRISMA flow diagram. The overall prevalence of the Mtb genotypes/sublineage in Iran was determined using the random effects or fixed effect model. The metafor R package and MedCalc software were employed for performing this meta-analysis.

Results

We identified 34 studies for inclusion in this study, containing 8329 clinical samples. Based on the pooled prevalence of the Mtb genotypes, NEW1 (21.94, 95% CI: 16.41–28.05%), CAS (19.21, 95% CI: 14.95–23.86%), EAI (12.95, 95% CI: 7.58–19.47%), and T (12.16, 95% CI: 9.18–15.50%) were characterized as the dominant circulating genotypes in Iran. West African (L 5/6), Cameroon, TUR and H37Rv were identified as genotypes with the lowest prevalence in Iran (< 2%). The highest pooled prevalence rates of multidrug-resistant strains were related to Beijing (2.52, 95% CI) and CAS (1.21, 95% CI).

Conclusions

This systematic review showed that Mtb populations are genetically diverse in Iran, and further studies are needed to gain a better insight into the national diversity of Mtb populations and their drug resistance pattern.

Molecular epidemiology of Mycobacterium tuberculosis isolates in Iran using spoligotyping

Spoligotyping can help assess the transmission of Mycobacterium tuberculosis strains. We aimed to study the genotyping of M. tuberculosis isolated from patients with tuberculosis from the west of Iran by spoligotyping. Forty-seven M. tuberculosis isolates were collected from the west of Iran. All samples were cultured on Löwenstein-Jensen medium incubated at 37°C for 8 weeks. Bacterial isolates were identified as M. tuberculosis using standard biochemical tests. Drug resistance patterns of M. tuberculosis to rifampicin and isoniazid were determined, and multidrug-resistant (MDR) strains were isolated. After DNA extraction, spoligotyping was performed. We found new spoligotypes 4162 and 4163, which correlated with atypical lineage. Atypical and unknown lineages also had correlations with the MDR tuberculosis rate (4%). The most prevalent spoligointernational types were orphan (34%), 2669 (23.4%) and 127 (14.8%) types. The most prevalent clades were Ural-2 (NEW-1) (25.53%) and atypical (23.40%) lineages. The predominant clade was Ural-2 (NEW-1) and an atypical lineage restricted to Iran. The rate of MDR was low. Knowledge of the circulating isolates in the west of Iran will help implement control programmes, so knowledge of the dynamic transmission of local isolates is crucial.

Genetic Diversity of Drug-resistant Mycobacterium tuberculosis Isolates in Isfahan Province of Iran

Background:

Increasing drug resistance is an important factor in the complexity of tuberculosis (TB) control. The identification of disease transmission type, recurrence of a previous infection, or new transmission of the disease is the key factor in the control of TB. In this study, we aimed to identify the genetic diversity of drug-resistant Mycobacterium tuberculosis isolates in Isfahan province of Iran through the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing method based on 24 loci.

Materials and Methods:

Of 300 isolates obtained from a variety of clinical specimens, 18 drug-resistance M. tuberculosis clinical isolates (resistant to a single drug to more than one drug) were collected between 2013 and 2015 from regional TB reference laboratory in Isfahan. All drug-resistance M. tuberculosis isolates were typed by 24-locus MIRU-VNTR typing.

Results:

The highest percentage of isolates, 38.8%, belonged to the East-Asian lineage (lineage 2), while the lineages Indo-Oceanic (lineage 1), East-African–Indian (lineage 3), and Euro-American (lineage 4) represented 5.5%, 22.2%, and 33.3%, respectively. Among the 33.3% (6/18) Euro-American strains, the Latin American– Mediterranean and Ural sub-lineage were 22.2% (4/18) and 11.1% (2/18), respectively.

Conclusion:

The results of this study show that the lineages of drug-resistant M. tuberculosis isolates in Isfahan province of Iran are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). Continued molecular monitoring is important as it has been proposed that the genetics and evolutionary backgrounds of drug-resistant M. tuberculosis strains may have an impact on the transmissibility profile.

Genetic Lineages of Mycobacterium tuberculosis Isolates in Isfahan, Iran

In this study, we aimed to identify the genetic lineages of Mycobacterium tuberculosis isolates in Isfahan via the mycobacterial interspersed repetitive-unit-variable number tandem repeat typing method based on 15 loci. Forty-nine M. tuberculosis isolates were collected between 2013 and 2015 from Tuberculosis patients in Mollahadi Sabzevari Tuberculosis Center in Isfahan. All isolates were typed by 15-locus MIRU-VNTR typing. The highest percentage of isolates, 44.89 % (22/49), belonged to the Euro-American lineage, while the frequencies of the East-African-Indian, East-Asian, and Indo-Oceanic lineages were 28.57 % (14/49), 24.4 % (12/49), and 2.04 % (1/49), respectively. Among the 22 isolates of the Euro-American lineage, those belonging to the NEW-1 sub-lineage were most prevalent (24.4 %). Approximately, the same proportion of isolates belonging to the Delhi/CAS, Beijing, and NEW-1 sub-lineages were identified in Iranian and Afghan immigrant patients. The Delhi/CAS and Beijing sub-lineage isolates were prevalent among patients who had been previously treated for TB. Results showed that all of the 49 MIRU-VNTR patterns were unique and the clustering rate of the 15-locus MIRU-VNTR was 0.0 (minimum recent transmission). The results of this study show that the lineages of M. tuberculosis isolates in Isfahan are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). The low clustering rate in our results reveals that transmission of tuberculosis in Isfahan is, in most cases, a reactivation of previous tuberculosis infection and the role of recently transmitted disease is minor.

Prevalence and occurrence rate of Mycobacterium tuberculosis Haarlem family multi-drug resistant in the worldwide population: A systematic review and meta-analysis

BACKGROUND

Transmission of Mycobacterium tuberculosis (M. tuberculosis) can occur in different ways. Furthermore, drug resistant in M. tuberculosis family is a major problem that creates obstacles in treatment and control of tuberculosis (TB) in the world. One of the most prevalent families of M. tuberculosis is Haarlem, and it is associated with drug resistant. Our objectives of this study were to determine the prevalence and occurrence rate of M. tuberculosis Haarlem family multi-drug resistant (MDR) in the worldwide using meta-analysis based on a systematic review that performed on published articles.

MATERIALS AND METHODS

Data sources of this study were 78 original articles (2002-2012) that were published in the literatures in several databases including PubMed, Science Direct, Google Scholar, Biological abstracts, ISI web of knowledge and IranMedex. The articles were systematically reviewed for prevalence and rate of MDR. Data were analyzed using meta-analysis and random effects models with the software package Meta R, Version 2.13 (P < 0.10).

RESULTS

Final analysis included 28601 persons in 78 articles. The highest and lowest occurrence rate of Haarlem family in M. tuberculosis was in Hungary in 2006 (66.20%) with negative MDR-TB and in China in 2010 (0.8%), respectively. From 2002 to 2012, the lowest rate of prevalence was in 2010, and the highest prevalence rate was in 2012. Also 1.076% were positive for MDR and 9.22% were negative (confidence interval: 95%).0020.

CONCLUSION

Many articles and studies are performed in this field globally, and we only chose some of them. Further studies are needed to be done in this field. Our study showed that M. tuberculosis Haarlem family is prevalent in European countries. According to the presence of MDR that was seen in our results, effective control programs are needed to control the spread of drug-resistant strains, especially Haarlem family.

Application of Deletion- Targeted Multiplex PCR technique for detection of Mycobacterium tuberculosis Beijing strains in samples from tuberculosis patients

BACKGROUND AND OBJECTIVE

Molecular epidemiological studies have shown that certain genotypes of Mycobacterium tuberculosis (MTB) are over-represented in limited geographical regions, suggesting of evolution of certain genotypes with increasing virulence and pathogenicity. Beijing strain of MTB was initially described by its potential to cause outbreaks worldwide and its association with drug resistance. Due to tuberculosis (TB)-related mortality which is associated with Beijing genotype, this study was designed with the aim to detect the MTB Beijing genotype in the region of study.

MATERIALS AND METHODS

A total of 170 clinical isolates of MTB were collected from the TB reference laboratory of Khuzestan province, Iran, over one year period from February 2010 to February 2011. Phenotypic tests were used for preliminary detection of MTB. Culture positive MTB isolates were confirmed by multiplex PCR based on IS6110 gene with subsequent screening for resistance to isoniazid (INH), and rifampin (RIF) by PCR using relevant primers. Three set of primers were used to differentiate Beijing from non-Beijing strains by using Deletion- Targeted Multiplex (DTM) PCR.

RESULTS

From 160 PCR-confirmed MTB isolates, 18 (11.25%) showed mutation in katG gene related to INH resistance and 20 (12.5%), associated with mutation in rpoB gene related to RIF resistance, and 8 (5%) were detected as Beijing strain using multiplex PCR. The majority of detected Beijing strains (6/8[75%]) comprised mutation in katG gene with the prevalent mutation specifically in codon 315. In 4 Beijing strains (2.5%), mutation in rpoB gene were also detected.

CONCLUSION

Using DTM- PCR, the rate of Beijing strains in the region of study was determined as 5%. Although for detection of MTB antimicrobial resistance, it is advised to use a combination of conventional antimicrobial susceptibility testing and molecular techniques, however for time saving, it seems that DTM-PCR, is a simple technique for use in areas of the world where Beijing strains are highly prevalent.

Spoligotyping and drug resistance patterns of Mycobacterium tuberculosis isolates from five provinces of Iran

Tuberculosis (TB) persists as a public health problem in Iran. Characterization of Mycobacterium tuberculosis isolates circulating in this area will contribute to understand and control the spread of the strains. The aims of this study were to understand the genetic diversity and drug susceptibility of M. tuberculosis isolates circulating in Iran and to analyze the relationship between genotype and drug resistance. A total of 291 M. tuberculosis isolates collected from TB patients were genotyped by spoligotyping. Drug susceptibility testing was performed using proportion method. Spoligotyping resulted in 75 distinct patterns. 86.2% of isolates were grouped in 35 clusters while the remaining isolates were unique. Ural was found to be the most predominant lineage (34.3%) followed by Central Asian strain (CAS) (24%), T (18.2%), Manu2 (7.5%) and Latin American-Mediterranean (LAM) (6.1%). The five largest clusters were Ural/Spoligotype International Type (SIT)127 (15.8%), CAS1/SIT26 (9.2%), T1/SIT53 (6.1%), T1/SIT284 (5.4%), and CAS1/SIT25 (4.4%). About 5% of isolates had multidrug resistance (MDR) and 10% had other resistance. MDR was significantly associated with Beijing strains, but not with Ural family. This study highlights dominance of Ural, CAS, and T families in Iran. Biogeographic specificity of CAS and T families to border provinces of Iran including Sistan-Baluchestan and Kermanshah, respectively, suggested that this family strains might be transmitted from these regions to other provinces of the country.

Assessment of the quality of dna extracted by two techniques from Mycobacterium tuberculosis for fast molecular identification and genotyping

We report a comparative study of two DNA extraction techniques, thermolysis and chemical lysis (CTAB), for molecular identification and genotyping of M. tuberculosis. Forty DNA samples were subjected to PCR and the results demonstrated that with thermolysis it is possible to obtain useful data that enables fast identification and genotyping.