Publications by authors named "Parissa Farnia"

76 Publications

Characterization of Clinical Isolates of Mycobacterium simiae Using Drug Susceptibility Tests and Molecular Analyses.

Curr Microbiol 2021 Apr 13. Epub 2021 Apr 13.

Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), World Health Organization Collaborating Centre, Shahid Beheshti University of Medical Sciences (Medical Campus), Darabad, PO 19575/154, Tehran, 19556, Iran.

Mycobacterium simiae is an emerging nontuberculous mycobacterium (NTM) and an opportunistic pathogen which is described mainly in Asia and presents in the environment that can cause pulmonary infection. The objective of this study is to characterize M. simiae clinical isolates using mycobacterial interspersed repetitive unit variable-number tandem repeats (MIRU-VNTR) typing for the differentiation of the strains. A total of 169 clinical isolates of NTM were recovered from patients suspected of having tuberculosis (TB)-like and related infections. After isolation and identification of mycobacterial strains by conventional biochemical and PCR-based tests, M. simiae strains were confirmed using restriction fragment length polymorphism (RFLP)-based identification assay. Furthermore, drug susceptibility and MIRU-VNTR typing was performed using on the clinical isolates of M. simiae. Out of 169 NTM strains, 92 (54.4%) isolates were identified as M. simiae. Antibiotic susceptibility experiments indicated that all 92 M. simiae isolates were resistant to first line antimycobacterial agents. Moreover, 8 (8.6%) M. simiae isolates were resistant to ciprofloxacin; and 6 (6.5%) were resistant to both amikacin and kanamycin, while the remaining were susceptible to second line antimycobacterial agents. MIRU-VNTR analysis showed that the M. simiae isolates were classified in four distinct M. simiae clusters and two single types. The minimum spanning analysis revealed that the isolates were grouped in three complexes. The data suggested that MIRI-VNTR typing is useful for typing of M. simiae isolates, however, MIRU-16 locus was absolutely absent in M. simiae.
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http://dx.doi.org/10.1007/s00284-021-02486-wDOI Listing
April 2021

An Overview of Genetic Information of Latent Mycobacterium tuberculosis.

Tuberc Respir Dis (Seoul) 2021 Jan 30;84(1):1-12. Epub 2020 Oct 30.

Mycobacteriology Research (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Mycobacterium tuberculosis has infected more than two billion individuals worldwide, of whom 5%-10% have clinically active disease and 90%-95% remain in the latent stage with a reservoir of viable bacteria in the macrophages for extended periods of time. The tubercle bacilli at this stage are usually called dormant, non-viable, and/or non-culturable microorganisms. The patients with latent bacilli will not have clinical pictures and are not infectious. The infections in about 2%-23% of the patients with latent status become reactivated for various reasons such as cancer, human immunodeficiency virus infection, diabetes, and/or aging. Many studies have examined the mechanisms involved in the latent state of Mycobacterium and showed that latency modified the expression of many genes. Therefore, several mechanisms will change in this bacterium. Hence, this study aimed to briefly examine the genes involved in the latent state as well as the changes that are caused by Mycobacterium tuberculosis. The study also evaluated the relationship between the functions of these genes.
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http://dx.doi.org/10.4046/trd.2020.0116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801807PMC
January 2021

Human genetic background in susceptibility to tuberculosis.

Int J Mycobacteriol 2020 Jul-Sep;9(3):239-247

Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Tuberculosis (TB), especially in developing countries, is a major threat to human health. The pathogenesis of TB remains poorly understood, and <5%-10% of individuals infected with Mycobacterium tuberculosis (MTB) will develop clinical disease. The human genetic factors contributing to susceptibility or resistance to TB pathogenesis have been investigated by high-throughput and low-throughput association studies. Genetic polymorphisms of several genes including TLR, IGRM, VDR, ASAP1, AGMO, FOXP1, and UBLCP1 effect on the disease phenotype and also the outcome of TB treatment. Recently, microRNAs (miRNAs), which negatively regulated gene expression at the posttranscriptionally level, have gained increasing attention due to their altered expression in various human diseases, including some infections. They are crucial posttranscriptional regulators of immune response in both innate and adaptive immunity. It has been established in recent studies that the host immune response against MTB is regulated by many miRNAs, most of which are induced by MTB infection. Moreover, differential expression of miRNAs in TB patients may help distinguish between TB patients and healthy individuals or latent TB. In this review, we summarize and discuss the literature and highlight the role of selected single nucleotide polymorphisms and miRNAs that have been associated with TB infection.
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http://dx.doi.org/10.4103/ijmy.ijmy_118_20DOI Listing
August 2020

Prevalence of Mycobacterium abscessus among the Patients with Nontuberculous Mycobacteria.

Arch Iran Med 2020 03 1;23(3):163-168. Epub 2020 Mar 1.

Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Background: Considering the importance of the increasing incidence of non-tuberculous mycobacteria, especially Mycobacterium abscessus worldwide, we conducted a study to evaluate the incidence of these diseases in our area. The aim of this study was to evaluate the prevalence of M. abscessus in patients with non-tuberculous mycobacteria.

Methods: This descriptive study was performed on 18,083 samples isolated from patients with non-tuberculous mycobacteria during 2011-2017 at the Mycobacteriology Research Center (MRC), Tehran, Iran. To identify the Mycobacterium species, a 439 bp fragment of the IS6110 gene was first amplified using primers TB1 and TB2. Samples with a negative polymerase chain reaction (PCR) result were analyzed to investigate non-tuberculosis mycobacteria (NTM), especially M. abscessus using the RFLP method.

Results: Of the 18,083 samples, 5513 (30.49%, 95% CI, 12.95) strains of Complex Tuberculosis and 236 (1.31%, 95% CI, 1.84) strains of NTM were identified. The mean age of the patients with NTM was 18 years, and most of them were male. The most commonly identified species in this study were M. abscessus type Ι 32 (13.56%, 95% CI, 18.36) and M. abscessus type II 13 (5.51%, 95%CI, 20.04).

Conclusion: In this study, we observed a high prevalence of Mycobacterium abscessus type 1 in patients. As the treatment protocol for non-TB mycobacteria is different from M. abscessus complex, the diagnosis of these species as soon as possible will be significant for physicians.
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March 2020

Drug-resistant Mycobacterium tuberculosis: Epidemiology and role of morphological alterations.

J Glob Antimicrob Resist 2018 03 16;12:192-196. Epub 2017 Oct 16.

Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden. Electronic address:

In this brief review, various forms of drug-resistant tuberculosis (DR-TB) are discussed. The focus of the study is to highlight morphological alterations of DR-TB bacilli at the cellular level.
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http://dx.doi.org/10.1016/j.jgar.2017.10.006DOI Listing
March 2018

Distribution scheme of antituberculosis drug resistance among HIV patients in a referral centre over 10 years.

J Glob Antimicrob Resist 2017 12 21;11:116-119. Epub 2017 Jul 21.

Clinical Tuberculosis and Epidemiology Research Center (CTERC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objectives: Antituberculosis drug resistance is increasing among tuberculosis (TB) patients globally, particularly in those who are human immunodeficiency virus (HIV)-positive. The aim of this study was to determine the pattern of anti-TB drug resistance in these patients in an effort to improve successful treatment outcomes with a proper regimen.

Methods: A cross-sectional study was conducted on adult TB/HIV co-infected patients from 2005-2015. The pattern of anti-TB drug resistance was evaluated among HIV-positive patients with and without a history of TB treatment. Categorisation was made as follows: isoniazid (INH)-resistant; rifampicin (RIF)-resistant; or multidrug-resistant (MDR).

Results: A total of 52 patients were enrolled in this study (median age 38 years). Among the 52 patients, 18 (34.6%) were MDR-TB patients and the rest were monoresistant TB (resistant either to INH or RIF). INH resistance was the most common resistance pattern (36.5%) noted among patients and was significantly associated with new TB cases (69% vs. 31%; P=0.01). During TB treatment, 3/48 patients (6.3%) failed treatment and 11/48 (22.9%) died. Patients with MDR-TB were more likely to die during treatment (44.4% vs. 10%; P=0.011).

Conclusions: Any drug resistance in previously treated TB cases among HIV-infected patients remains high. The risk of death is increasing in MDR-TB/HIV co-infected patients.
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http://dx.doi.org/10.1016/j.jgar.2017.06.010DOI Listing
December 2017

Association of Interferon- Receptor-1 Gene Polymorphism with Nontuberculous Mycobacterial Lung Infection among Iranian Patients with Pulmonary Disease.

Am J Trop Med Hyg 2017 Jul;97(1):57-61

Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Nontuberculous mycobacteria (NTM) cause significant pulmonary infections in humans. Researchers have reported an association between interferon-gamma receptor-1 (IFN-R1 or IFNGR1) deficiency and susceptibility to NTM, but the relevance of polymorphism within these genes is not yet clear. In this study, a single nucleotide polymorphism (SNP), T to C, at position-56 in NTM patients with pulmonary disease was investigated. Molecular identification of isolates was performed with genes using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). Then, the host genomic DNA from confirmed NTM patients ( = 80) and control subjects ( = 80) were screened for SNPs of IFNGR1 (T-56C) by PCR-RFLP. The results indicated that NTM patients had higher TC (26/80; 32.5%) or CC (46/80; 57.5%) genotypes in comparison with control groups (TC genotypes [22/80, 27.5%]; CC genotypes [6/80, 7.5%]) ( < 0.05). In this regard, all the patients infected with rapid-growing (RGM, i.e., and ) had CC genotypes (100%). In contrary, only 50.7% (35/69) of infected patients with slow-growing (i.e., , , and ) had CC genotypes. Thus, patients with CC mutation in IFNGR1 at position-56 are more likely to develop RGM infection. In overall, there is a significant association between SNP of IFNGR1 at position-56 and susceptibility to NTM infection. Based on these data, we propose SNP of IFNGR1 at position-56 as a suitable "biomarker" for identifying populations at higher risk of infection.
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http://dx.doi.org/10.4269/ajtmh.16-0905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508906PMC
July 2017

Bovis Bacillus Calmette-Guerin (BCG) infection induces exosomal miRNA release by human macrophages.

J Transl Med 2017 05 12;15(1):105. Epub 2017 May 12.

Airways Disease Section, National Heart & Lung Institute, Imperial College London, London, UK.

Background: Tuberculosis (TB) remains a significant global health concern and its diagnosis is challenging due to the limitations in the specificity and sensitivity of the current diagnostic tests. Exosomes are bioactive 30-100 nm vesicles produced by most cell types and are found in almost all human body fluids. Exosomal microRNAs (miRNAs) can transfer biological information between cells and tissues and may act as potential biomarkers in many diseases. In this pilot study, we assessed the miRNA profile of exosomes released from human monocyte-derived macrophages upon infection with Mycobacterium bovis Bacillus Calmette-Guerin (BCG).

Methods: Human monocytes were obtained from the peripheral blood of three healthy subjects and driven to a monocyte-derived macrophage (MDM) phenotype using standard protocols. MDMs were infected with BCG or left uninfected as control. 72 h post-infection, exosomes were collected from the cell culture medium, RNA was isolated and RNA-seq performed. The raw reads were filtered to eliminate adaptor and primer sequences and the sequences were run against the mature human miRNA sequences available in miRBase. MicroRNAs were identified using an E value <0.01. miRNA network analysis was performed using the DIANA miRNA tool, miRDB and functional KEGG pathway analysis.

Results: Infection of MDMs with BCG leads to the release of several exosomal miRNAs. These included miR-1224, -1293, -425, -4467, -4732, -484, -5094, -6848-6849, -4488 and -96 all of which were predicted to target metabolism and energy production-related pathways.

Conclusions: This study provides evidence for the release of specific exosomal miRNAs from BCG-infected MDMs. These exosomal miRNAs reflect host-pathogen interaction and subversion of host metabolic processes following infection.
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http://dx.doi.org/10.1186/s12967-017-1205-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427544PMC
May 2017

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Nat Genet 2017 Mar 16;49(3):395-402. Epub 2017 Jan 16.

Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts, USA.

Multidrug-resistant tuberculosis (MDR-TB), caused by drug-resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. Here we examined a data set of whole-genome sequences from 5,310 M. tuberculosis isolates from five continents. Despite the great diversity of these isolates with respect to geographical point of isolation, genetic background and drug resistance, the patterns for the emergence of drug resistance were conserved globally. We have identified harbinger mutations that often precede multidrug resistance. In particular, the katG mutation encoding p.Ser315Thr, which confers resistance to isoniazid, overwhelmingly arose before mutations that conferred rifampicin resistance across all of the lineages, geographical regions and time periods. Therefore, molecular diagnostics that include markers for rifampicin resistance alone will be insufficient to identify pre-MDR strains. Incorporating knowledge of polymorphisms that occur before the emergence of multidrug resistance, particularly katG p.Ser315Thr, into molecular diagnostics should enable targeted treatment of patients with pre-MDR-TB to prevent further development of MDR-TB.
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http://dx.doi.org/10.1038/ng.3767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402762PMC
March 2017

Comparison of single nucleotide polymorphisms [SNP] at TNF-α promoter region with TNF receptor 2 (TNFR2) in susceptibility to pulmonary tuberculosis; using PCR-RFLP technique.

Am J Clin Exp Immunol 2016 30;5(4):55-61. Epub 2016 Nov 30.

Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences Tehran, Iran.

Since apoptosis and survival of the immune cells are crucially important in prevention or predisposition of individual from/to infections, especially in intracellular ones, the current study was performed to assess the correlation of host genetic polymorphisms with susceptibility to TB. For this reason, we investigated the difference of the single nucleotide polymorphisms [SNPs] in tumor necrosis factors [TNF-α] genes at (-238, -308, -857 and -863 position) and tumor necrosis factors receptors two [TNFR2] at (T 587 G position) between patients [n=151] and control [n=83]. The genotyping was studied by using PCR-RFLP which had high sensitivity in detecting compared with other techniques. The results showed a strong correlation between two polymorphisms in different loci of TNF-α gene including TNF-α T-857 C and A 238 G. But no association were found in TNFR2 genes with susceptibility to TB. And we found no correlation between TNFR2 and TNF-α gene polymorphisms. Therefore, the TNF-α T 857 C and A 238 G SNPs could be promising marker for identifying risk populations.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5218852PMC
November 2016

Deletion of region of difference 181 in Mycobacterium tuberculosis Beijing strains.

Int J Mycobacteriol 2016 Dec 25;5 Suppl 1:S238-S239. Epub 2016 Nov 25.

Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objectives/background: The region of differences (RDs) polymorphisms is a potential molecular epidemiology method to distinguish origins of Mycobacterium tuberculosis. To date, 68 RDs have been identified in M. tuberculosis. This study was designed to determine the frequency of RD deletions in M. tuberculosis strains that were isolated from patients with pulmonary tuberculosis who were referred to the National Research Institute of Tuberculosis and Lung Disease for diagnosis and treatment. Therefore, highly polymorphic regions (RD1, RD150, and RD181) among M. tuberculosis strains isolates were investigated.

Methods: A total of 250 M. tuberculosis isolates were identified by conventional and molecular methods. Subsequently, spoligotyping and RD typing (RD1, RD150 and RD181) were performed to genotype these strains.

Results: The most frequent spoligotype belonged to Haarlem (n=85, 34.0%) followed by CAS (n=54, 21.6%), T1 (n=27, 10.8%), and Beijing (n=28, 11.2%) lineages. Deletion in RD181 was identified only among the Beijing lineage (Fig. 1).

Conclusion: As we found a deletion in RD181 in the Beijing strains only, we propose to use this marker as an identification tool for genotyping of the Beijing strain.
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http://dx.doi.org/10.1016/j.ijmyco.2016.09.071DOI Listing
December 2016

Molecular drug susceptibility testing against the first-line (rifampin and isoniazid) and second-line (ciprofloxacin-amikacin and kanamycin) treatment in different subtypes of Mycobacterium simiae.

Int J Mycobacteriol 2016 Dec 22;5 Suppl 1:S215. Epub 2016 Nov 22.

Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objective Background: Mycobacterium simiae has been identified as the most prevalent slow growing mycobacteria that has been isolated among Iranian patients. Due to an importance of molecular approaches in the treatment of nontuberculosis mycobacteria, this study aimed to evaluate molecular drug susceptibility testing against the first-line (rifampin and isoniazid) and second-line (ciprofloxacin-amikacin and kanamycin) treatment in different subtypes of M. simiae.

Methods: The study involved all patients presenting to our referral tuberculosis center from March 2014 to August 2016, with confirmation of M. Simiae. For all sputum samples, after digestion and decontamination, followed by DNA extraction, polymerase chain reaction-restriction fragment length polymorphism was performed using the hsp65 gene. Furthermore, susceptibility to rifampin, isoniazid, ciprofloxacin, amikacin, and kanamycin were evaluated using rpoB, inhA, katG, gyrA, and rrs genes, respectively.

Results: In total, 60 cases (58.33% men and 41.66% women) of M. simiae infections were identified and all were confirmed as subtype I. All the patients were resistant to the first line-tuberculosis drugs, while 88.33% and 91.66% of cases were susceptible to ciprofloxacin and both amikacin and kanamycin, respectively.

Conclusion: Regarding the given result, first-line tuberculosis drugs should be excluded from the treatment regimen of M. simiae patients. In addition, subtype I seems to be the most or even the only isolated M. simiae subtype among all Iranian patients. While both amikacin and kanamycin drugs showed better efficacy in the treatment M. simiae, the most susceptible antibiotic is still indeterminate.
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http://dx.doi.org/10.1016/j.ijmyco.2016.11.006DOI Listing
December 2016

Identification of different subtypes of rapid growing Atypical Mycobacterium from water and soil sources: Using PCR-RFLP using hsp65 and rRNA 16s-23s genes.

Int J Mycobacteriol 2016 Dec 14;5 Suppl 1:S212-S213. Epub 2016 Nov 14.

Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objective/background: Nontuberculosis mycobacteria (NTM) are a diverse group of microorganisms that cause a variety of diseases in humans including skin, respiratory, and gastrointestinal tract infection. Generally, NTM are classified into two categories: rapid (<7days) and slow growing (>7days). In this study, we aimed to investigate NTM frequency and prevalence in environmental samples. Additionally, we tried to identify various subtypes of isolated rapid growing mycobacteria (RGM).

Methods: Through a prospective descriptive cross-sectional study, water and soil samples were gathered from four neighboring towns around Tehran, the capital of Iran, at different geographic directions. Every 100m of the studied areas gave one sample containing 6g of soil in 3-5cm depth deposited in 50mL sterile water as sampling media. After digestion and decontamination, DNA from culture-positive specimens (RGM) were extracted using phenol-chloroform methods. Then the molecular identification of species and subspecies were performed using 16s-23s rRNA and hsp65 gene.

Results: In total, 341 RGM were found, out of which 322 (94.4%) were identified and 20 (5.8%) could not be identified. The most frequent RGM was, Mycobacterium fortuitum (72; 22%), Mycobacterium senegalense (58; 17.7%), Mycobacterium parafortuitum (44; 13.4%) and Mycobacterium conceptionense type 1 (24; 7.2%), and Mycobacterium cheloni type 1 (20; 6.0%). As shown in Table 1, M. fortuitum had more subtypes (8), and the frequency of subtypes 1 (27.7%), 4 (16.6%), and 5 (13.8%) were higher. Among subtypes of M. senegalense, subtype 1 had a higher frequency (70.4%) in comparison to subtype 2 (29.5%). M. cheloni had just one subtype.

Conclusion: Our results showed M. fortuitum as the most prominent strain isolated from environmental samples. The frequency was similar in different places, irrespective of climatic variations. Availability of various subtypes of M. fortuitum might indicate a large circulation of this RGM in soil and water of Iranian territory. This high prevalence of M. fortuitum might raise the risk infection, especially in children, immunocompromised patients, diabetics, and cancer cases.
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http://dx.doi.org/10.1016/j.ijmyco.2016.09.057DOI Listing
December 2016

Investigation of urine lipoarabinomannan in human immunodeficiency virus patients with or without coinfection with Tuberculosis in Iran.

Int J Mycobacteriol 2016 Dec 22;5 Suppl 1:S186-S187. Epub 2016 Nov 22.

Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran; Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

Objective/background: Tuberculosis (TB) remains the leading cause of AIDS-related deaths among adults in countries with resource limitations. The emergence of the Xpert MTB/RIF rapid molecular assay and its subsequent World Health Organization endorsement in 2010 transformed the TB-diagnostic landscape. Xpert provided diagnostic accuracy that was far superior to that of the sputum-smear microscopy test previously used. The detection of mycobacterial lipoarabinomannan (LAM) antigen in urine has emerged as a potential point-of-care test for TB. LAM antigen is a lipopolysaccharide present in mycobacterial cell walls which is released from metabolically active or degenerating bacterial cells and appears to be present only in people with active TB. Urine-based testing has advantages over sputum-based testing because urine is easy to collect and store and lacks the infection control risks associated with sputum collection. A previously study reported that urinary-LAM testing is a rapid, low-cost, ante-mortem diagnosis for human immunodeficiency virus (HIV)-associated TB. The objective of this study was to investigate the levels of LAM in HIV patients referred to the Mashih Daneshvari Hospital Tehran, Iran.

Methods: Urine from 31 HIV patients without TB, 33 HIV patients with pulmonary TB, and eight HIV patients with extrapulmonary TB was analyzed for LAM using enzyme-linked immunosorbent assay kits (Mybiosource, San Diego, CA, USA).

Results: The plasma levels of LAM in pulmonary TB/HIV patients was 7.67±2.3ng/ml compared with 4.5±1.6ng/ml in extrapulmonary TB/HIV and 6.7±1.2ng/ml in HIV patients without TB. There was no significant difference in urine LAM levels between the three groups.

Conclusion: Our results highlight the limitations of using urine LAM levels for differentiating HIV-associated TB patients in Iran.
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http://dx.doi.org/10.1016/j.ijmyco.2016.11.005DOI Listing
December 2016

Overview of drug-resistant tuberculosis worldwide.

Int J Mycobacteriol 2016 Dec 11;5 Suppl 1:S161. Epub 2016 Nov 11.

Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Even in the 21st century, we are losing the battle against eradication of tuberculosis (TB). In 2015, 9.6 million people were estimated to have fallen ill with TB, of which 1.5 million people died. This is the real situation despite the well-structured treatment programs and availability of effective treatment options since the 1950s. The high mortality rate has been associated with other risk factors, such as the HIV epidemic, underlying diseases, and decline of socioeconomic standards. Furthermore, the problem of drug resistance that was recognized in the early days of the chemotherapeutic era raises serious concerns. Although resistance to a single agent is the most common type, resistance to multiple agents is less frequent but of greater concern. The World Health Organization estimated approximately 5% of all new TB cases involved multidrug-resistant (MDR)-TB. The estimation for MDR-TB is 3.3% for new cases, and 20.5% for previously treated cases. Failure to identify and appropriately treat MDR-TB patients has led to more dangerous forms of resistant TB. Based on World Health Organization reports, 5% of global TB cases are now considered to be extensively drug resistant (XDR), defined as MDR with additional resistance to both fluoroquinolones and at least one second-line injectable drug. XDR-TB had been reported by 105 countries by 2015. An estimated 9.7% of people with MDR-TB have XDR-TB. More recently, another dangerous form of TB bacillus was identified, which was named totally drug resistant (TDR-TB) or extremely drug resistant TB. These strains were resistant to all first- and second-line anti-TB drugs. Collectively, it is accepted that 2% of MDR-TB strains turn to be TDR-TB. This number, however, may not reflect the real situation, as many laboratories in endemic TB countries do not have proper facilities and updated protocols to detect the XDR or TDR-TB strains. Nevertheless, existing data emphasize the need for additional control measures, such as new diagnostic methods, better drugs, and more effective vaccines to prevent the spread of these strains around the world.
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http://dx.doi.org/10.1016/j.ijmyco.2016.09.066DOI Listing
December 2016

HIV and tuberculosis trends and survival of coinfection in a referral center in Tehran: A 12-year study.

Int J Mycobacteriol 2016 Dec 27;5 Suppl 1:S16-S17. Epub 2016 Oct 27.

Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objective/background: The risk of mortality and morbidity among tuberculosis (TB) and human immunodeficiency virus (HIV) coinfected patients is significantly higher than that of patients infected with TB alone. The aim of this study was to evaluate the survival of TB-HIV patients in a TB-referral center during a 10-year follow-up.

Methods: All TB-HIV patients in our referral center were enrolled in the study from 2003 to 2014, and patients were divided into two groups: HIV-TB patients without a history of TB treatment (new cases of TB) and HIV-TB patients with a history of TB treatment. Both groups were treated based on World Health Organization TB-treatment guidelines, and multivariate analysis was performed to evaluate risk factors of all-cause mortality.

Results: During the study, 22 HIV-TB patients with a history of TB treatment and 263 HIV-TB patients with newly diagnosed TB were included. Baseline demographic and clinical characteristics were similar, except that miliary TB (98% vs. 2%) and mortality (97% vs. 3%; p=0.06) were more likely in HIV patients with newly diagnosed TB. During TB treatment and subsequent follow-up, two patients did not respond to treatment and 92 (32.3%) patients died, whereas the cure rate was 60%. Pneumothorax [hazard ratio (HR): 3.17], coinfection (herpes zoster, toxoplasmosis, cytomegalovirus infection, Pneumocystis jiroveci, candidiasis, and other opportunistic infection; HR: 1.75), CD4<100cells/mL (HR: 1.96), thrombocytopenia (HR: 2.29), and lack of treatment with antiretroviral agents (ART; HR: 2.82) were significantly associated with all-cause mortality according to multivariate analysis.

Conclusion: Our retrospective review of coinfected TB-HIV patients hospitalized in Tehran showed that the management and monitoring of coinfection, pneumothorax and other adverse effects, as well as early initiation of ART, improved patient survival.
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http://dx.doi.org/10.1016/j.ijmyco.2016.10.010DOI Listing
December 2016

Molecular genetics of Mycobacterium tuberculosis resistant to aminoglycosides and cyclic peptide testing by MTBDRsl in Armenia.

Int J Mycobacteriol 2016 Dec 12;5 Suppl 1:S159-S160. Epub 2016 Aug 12.

Ministry of Health of National Tuberculosis Control Program SNPO, Abovyan, Armenia.

Objective/background: The GenoType MTBDRsl test rapidly detects resistance to ethambutol, fluoroquinolones, second-line aminoglycosides (amikacin [AMK] and kanamycin [KAN]), and cyclic peptides (capreomycin [CAP]) in Mycobacterium tuberculosis. According to data from Global Drug Resistance Surveillance Report (2007), Armenia is counted as a high-burden country for multidrug-resistant tuberculosis (MDR-TB). The estimated burden of MDR-TB in 2012 was 9.4 (7-12) and 43 (38-49) among retreatment TB cases. A total of 92 laboratory confirmed cases were reported to the World Health Organization (57 new and 35 previously treated) out of 511 cases tested for MDR-TB.

Methods: A set of 77 drug-resistant TB isolates during 2011 and 2012 period, being either acid-fast bacterium positive or negative but culture-positive resistant to isoniazid, rifampin, or both according to the GenoType MTBDR plus assay, were consecutively tested using GenoType MTBDRsl. rrs gene analysis and the results from GenoType MTBDRsl were compared with phenotypic drug resistance testing. The DNA preparation method was performed as recommended by the manufacturer (Genotype MTBDR plus version 1.0 and Genotype MTBDRsl version 2.0 Hain Lifescience Nehren, Germany).

Results: Aminoglycosides are key drugs for the treatment of MDR-TB. A total of 77 drug-resistant TB and four extensively drug-resistant M. tuberculosis isolates from Armenian TB patients were analyzed to characterize mutations within rrs and to compare with phenotypic drug resistance testing. Simultaneously, the following were identified: 65 (84.41%) rrs wild type (WT), 1 (1.3%) rrs WT MUT1 and MUT2 (WT; A1401G and G1484T), 1 (1.3%) rrs WT1, MUT1 (A1401G), 9 (11.7%) rrs WT1, MUT1 (A1401G), and 1 (1.3%) rrs WT1, MUT1. Mutation at position 1401 in rrs leads to resistance to KAN (7/77=9%), AMK (9/77=11.68%), and CAP (5/77=6.49%). Eleven (14.28%) streptomycin-resistant strains had a rrs mutation.

Conclusion: Isolates with rrs structural gene mutations were cross-resistant to streptomycin, KAN, CAP, and AMK. Detection of the A1401G mutation appeared to be 100% specific for the detection of resistance to KAN and AMK. Being the first assessment, these data establish the presence of phenotypic drug-resistant and extensively drug-resistant strains using molecular profiling and are helpful in understanding aminoglycoside resistance on a molecular level.
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http://dx.doi.org/10.1016/j.ijmyco.2016.07.010DOI Listing
December 2016

Susceptibility to pulmonary tuberculosis: host genetic deficiency in tumor necrosis factor alpha (TNF-α) gene and tumor necrosis factor receptor 2 (TNFR2).

Int J Mycobacteriol 2016 Dec 12;5 Suppl 1:S136-S137. Epub 2016 Nov 12.

Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Objective/background: The susceptibility to tuberculosis (TB) depends upon different factors, and the risk of developing diseases after infection with Mycobacterium tuberculosis ranges from 5% to 10%. This suggests that besides the mycobacterial itself, the host genetic factors may determine the differences in host susceptibility to TB. Among the important risk factors, cytokines and especially tumor necrosis factor alpha (TNF-α) genes, are thought to be responsible for regulating the protective immune responses. The TNF-α gene that encodes the cytokines TNF-α is located within the class III region of the major histocompatibility complex (MHC). The TNF-α gene and its receptors have significant suppressive effects on bacterial growth into macrophages. Tumor necrosis factor receptor 1 (TNFR1) is more responsible when apoptosis is needed but tumor necrosis factor receptor 2 (TNFR2) is involved in cell survival. TNF-α conducts its replicative effects on immune cells via the latter. Up to now, several polymorphisms within the promoter region of the TNF-α gene have been shown to be associated with susceptibility or resistance to TB in different ethnic groups. By contrast, the correlation of TNF-α gene with their receptors such as TNFR2 in susceptibility to TB has not been resolved yet. In this study, we aimed to analyze the single nucleotide polymorphisms (SNPs) in the TNF-α gene at the -238, -308, -857, and -863 positions, and compare the susceptibility to TB with polymorphisms at TNFR2 (T587G).

Methods: One hundred fifty-one tuberculosis patients (n=151) and 83 control subjects (n=83) were included in this study. Polymorphisms in the TNF promoter region, namely TNF (SNP), -238, -308, -857, and -863 were studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). For TNFR2 polymorphisms at 587 positions, the following primers were used to amplify a 242 base pair (bp) product: 5'-TTCTGGAGTTGGCTGCGTGT-3' and ACTCTCCTATCCTGCCTGCT-3'. PCR products of TNFR2 digested with 2U enzymes of NLA III.

Results: The current study found a strong correlation between two polymorphisms in different loci of TNF-α gene including 857 C/C (85; 56.2%) and TNF 238 A/A 127 (84.1%). However, there were no associations between polymorphisms of the TNF-α gene and its receptor, that is, TNFR2.

Conclusion: Concerning our current study, screening assessments for TNF-α-857 and A238GSNPs in Iran would be important in order to make future decisions for preventive treatments before getting the disease among individuals who are at high risk considering their genotyping.
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http://dx.doi.org/10.1016/j.ijmyco.2016.09.038DOI Listing
December 2016

Molecular detection of fluoroquinolone resistance-associated gyrA mutations in ofloxacin-resistant clinical isolates of Mycobacterium tuberculosis from Iran and Belarus.

Int J Mycobacteriol 2016 09 3;5(3):299-305. Epub 2016 Aug 3.

Institute for Pulmonology and Phthisiology, Minsk, Belarus.

Objective/background: Detection of mutations in the quinolone resistance-determining region (QRDR) of the gyrA gene could determine resistance to fluoroquinolone antituberculosis drugs. The aim of this study was to detect mutations in QRDRs.

Methods: From 184 clinical isolates of Mycobacterium tuberculosis, ofloxacin resistance was proven in 42 isolates using the proportion method. The molecular basis of resistance to ofloxacin were investigated by the determination of mutations in the QRDR region of the gyrA gene. Extracted DNA fragments of 194bp from the gyrA gene were amplified and an automatic DNA sequencer was used for the sequencing process.

Results: Molecular genetic analysis of 42 resistant M. tuberculosis strains demonstrated that they belong to Principal Genetic Group (PGG) 1 in 19 cases (45.2±10.9%), to PGG2 in 15 cases (35.7±10.5%), and to PGG3 in eight cases (19.0±8.4%). Isolates from PGG1 were dominant among resistant isolates (P<.05). It was found that 24 (57%) resistant isolates carried mutations at codon 94 with five different amino acid changes: D94A (n=11), D94G (n=3), D94T (n=4), D94A (n=4), and D94Y (n=2). The remaining 18 (43%) isolates had mutations in codon A90V (GCG→GTG) and S91P (TCG→CCG). Five isolates had two mutations in codons 90 and 94. There was no difference between mutations at these two codons in resistant isolates of the two countries (P<.001). There was no polymorphism observed in codon 95 in any of the ofloxacin-susceptible isolates.

Conclusion: It was concluded that the determination of nucleotide sequences of QRDRs can be used as a molecular test for the rapid detection of ofloxacin resistance. Furthermore, frequencies in gyrA codons in Belarus and Iran were similar, therefore it is not of geographical concern for the two countries.
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http://dx.doi.org/10.1016/j.ijmyco.2016.07.004DOI Listing
September 2016

Impact of diabetes mellitus on tuberculosis drug resistance in new cases of tuberculosis.

J Glob Antimicrob Resist 2016 03 13;4:1-4. Epub 2015 Dec 13.

Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

The objectives of this study were to determine the impact of diabetes mellitus (DM) on antituberculosis drug resistance in new cases of tuberculosis (TB). A case-control study was conducted on all newly diagnosed pulmonary TB adult patients with DM as cases and without DM as controls who were hospitalised from May 2013 to October 2013 in Iran. A molecular resistance test for rapid detection of resistance to isoniazid and rifampicin was done. Multivariate analysis was performed to determine the impact of DM on any anti-TB drug resistance. In total, 62 TB cases with DM and 64 TB cases without DM were included. TB cases with DM were more likely to be older (59 years vs. 43 years; P=0.001). Two TB-DM patients had multidrug-resistant TB (MDR-TB) (3.2%) compared with no cases of MDR-TB in the control group, and more TB-DM cases had isolates that were resistant to at least one drug (12.9% vs. 10.9%). DM [odds ratio (OR)=4.82, 95% confidence interval (CI) 1-23.57], age <40 years (OR=5.48, 95% CI 1.19-25.29) and history of TB contact (OR=5.86, 95% CI 1.69-20.36) remained significantly associated with any drug resistance in the multivariate analysis. In conclusion, new TB patients with DM are at increased risk of anti-TB drug resistance. More studies are needed to confirm these results.
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http://dx.doi.org/10.1016/j.jgar.2015.11.006DOI Listing
March 2016

Association of IFN-γ and P2X7 Receptor Gene Polymorphisms in Susceptibility to Tuberculosis Among Iranian Patients.

Acta Microbiol Immunol Hung 2016 Mar;63(1):93-101

Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences , Tehran , Iran.

Interferon-gamma (IFN-γ) and P2X7 receptor are crucial for host defence against mycobacterial infections. Recent studies have indicated that IFN-γ, IFN-γ receptor 1 (IFN-γR1) andP2X7 gene polymorphisms are associated with susceptibility to pulmonary tuberculosis (TB). However, the relationship between IFN-γ and P2X7 polymorphism and TB susceptibility remains inconclusive in Iranian population. For this reason, single nucleotide polymorphisms (SNPs) in IFN-γ (G+2109A), IFN-γR1 (G-611A) and P2X7 genes (at -762, 1513 position) in patients (n = 100) were assessed using PCR-RFLP. Data were analysed with SPSS version 18. For the 2109 loci of IFN-γ gene, the frequency of mutant alleles between patients and controls were not statistically significant. However, there was a significant difference between the TB patient and controls for -611 alleles of IFN-γR1 (P = 0.01). Additionally, the frequency of P2X7 gene polymorphisms (SNP-762 and 1513) between patients and controls was statistically significant. In conclusions, our study revealed a significant association of IFN-γR1 and P2X7 genes polymorphisms with risk of developing TB in Iranian population.
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http://dx.doi.org/10.1556/030.63.2016.1.7DOI Listing
March 2016

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.

Int J Mycobacteriol 2016 Mar 28;5(1):66-73. Epub 2015 Dec 28.

Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic address:

Objective/background: Mycobacterium tuberculosis (MTB) causes active tuberculosis (TB) in only a small percentage of infected people. In most cases, the infection is clinically latent, where bacilli can persist in human hosts for years without causing disease. Surprisingly, the biology of such persister cells is largely unknown. This study describes the isolation, identification, and whole-genome sequencing (WGS) of latent TB bacilli after 782days (26months) of latency (the ability of MTB bacilli to lie persistent).

Methods: The in vitro double-stress model of latency (oxygen and nutrition) was designed for MTB culture. After 26months of latency, MTB cells that persisted were isolated and investigated under light and atomic force microscopy. Spoligotyping and WGS were performed to verify the identity of the strain.

Results: We established a culture medium in which MTB bacilli arrest their growth, reduce their size (0.3-0.1μm), lose their acid fastness (85-90%) and change their shape. Spoligopatterns of latent cells were identical to original H37Rv, with differences observed at spacers two and 14. WGS revealed only a few genetic changes relative to the already published H37Rv reference genome. Among these was a large 2064-bp insertion (RvD6), which was originally detected in both H37Ra and CDC1551, but not H37Rv.

Conclusion: Here, we show cell-wall free cells of MTB bacilli in their latent state, and the biological adaptation of these cells was more phenotypic in nature than genomic. These cell-wall free cells represent a good model for understanding the nature of TB latency.
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http://dx.doi.org/10.1016/j.ijmyco.2015.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443679PMC
March 2016

Nontuberculous mycobacteria in Middle East: Current situation and future challenges.

Int J Mycobacteriol 2015 Mar 10;4(1):7-17. Epub 2015 Jan 10.

Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, USA. Electronic address:

Nontuberculous mycobacteria (NTM) are a diverse group of bacterial species that are distributed in the environment. Many of these environmental bacteria can cause disease in humans. The identification of NTM in environmental sources is important for both clinical and epidemiological purposes. In this study, the distribution of NTM species from environmental and clinical samples in the Middle East was reviewed. In order to provide an overview of NTM, as well as recent epidemiological trends, all studies addressing NTM in the Middle East from 1984 to 2014 were reviewed. A total of 96 articles were found, in which 1751 NTM strains were isolated and 1084 of which were obtained from clinical samples, 619 from environmental samples and 48 were cited by case reports. Mycobacterium fortuitum was the most common rapid growing mycobacteria (RGM) isolated from both clinical (269 out of 447 RGM; 60.1%) and environmental (135 out of 289 RGM; 46.7%) samples. Mycobacterium avium complex (MAC) was the most common slow growing mycobacteria (SGM) isolated from clinical samples (140 out of 637 SGM; 21.9%). An increasing trend in NTM isolation from the Middle East was noted over the last 5years. This review demonstrates the increasing concern regarding NTM disease in the Middle East, emphasizing the need for regional collaboration and coordination in order to respond appropriately.
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http://dx.doi.org/10.1016/j.ijmyco.2014.12.005DOI Listing
March 2015

Nontuberculous Mycobacteria Isolation from Clinical and Environmental Samples in Iran: Twenty Years of Surveillance.

Biomed Res Int 2015 28;2015:254285. Epub 2015 May 28.

Section of Pulmonary, Critical Care, Sleep and Allergy Department of Medicine M/C 719, University of Illinois at Chicago, 840 S. Wood Street, Chicago, IL 60612-7323, USA.

Nontuberculous mycobacteria (NTM) are opportunistic pathogens that are widely distributed in the environment. There is a lack of data on species distribution of these organisms from Iran. This study consists of a review of NTM articles published in Iran between the years 1992 and 2014. In this review, 20 articles and 14 case reports were identified. Among the 20 articles, 13 (65%) studies focused on NTM isolates from clinical specimens, 6 (30%) studies examined NTM isolates from environmental samples, and one (5%) article included both clinical and environmental isolates. M. fortuitum (229/997; 23%) was recorded as the most prevalent and rapid growing mycobacteria (RGM) species in both clinical (28%) and environmental (19%) isolated samples (P < 0.05). Among slow growing mycobacteria (SGM), M. simiae (103/494; 21%) demonstrated a higher frequency in clinical samples whereas in environmental samples it was M. flavescens (44/503; 9%). These data represent information from 14 provinces out of 31 provinces of Iran. No information is available in current published data on clinical or environmental NTM from the remaining 17 provinces in Iran. These results emphasize the potential importance of NTM as well as the underestimation of NTM frequency in Iran. NTM is an important clinical problem associated with significant morbidity and mortality in Iran. Continued research is needed from both clinical and environmental sources to help clinicians and researchers better understand and address NTM treatment and prevention.
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http://dx.doi.org/10.1155/2015/254285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477424PMC
April 2016

Nontuberculous Mycobacteria: Epidemiologic, Mycobacteriologic, and Clinical Aspects.

Biomed Res Int 2015 16;2015:523697. Epub 2015 Jun 16.

Department of Health Science, University of Milano-Bicocca, San Gerardo Hospital, Via Pergolesi 33, 20900 Monza, Italy.

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http://dx.doi.org/10.1155/2015/523697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486753PMC
February 2016

Response.

Chest 2015 Apr;147(4):e158-e159

Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL. Electronic address:

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http://dx.doi.org/10.1378/chest.14-3235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388128PMC
April 2015

Co-infection of Mycobacterium tuberculosis and Pneumocystis jirovecii in the Iranian Patients With Human Immunodeficiency Virus.

Jundishapur J Microbiol 2015 Feb 20;8(2):e17254. Epub 2015 Feb 20.

Iranian HIV/AIDS Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, IR Iran.

Background: Based on the authors' knowledge, there is no study on the co-infection of opportunistic agents such as Mycobacterium tuberculosis and Pneumocystis jirovecii in the lungs of Iranian patients with immunosuppression.

Objectives: The current study aimed to show the rate of co-infection of M. tuberculosis and P. jirovecii in patients with Human Immunodeficiency Virus (HIV).

Patients And Methods: Forty-five pulmonary samples were collected from 30 patients with HIV who also infected with Tuberculosis and Pneumonia. All of the patients were admitted to two university hospitals of Mycobacteriology and the Iranian HIV/AIDS research centers. DNA of P. jirovecii was detected using nested-Polymerase Chain Reaction (nested-PCR) assay.

Results: All of the patients were male with the mean age of 32.95 ± 7.15 years. The mean of CD4 cell count was 109.25 cell/mm(3). Of 30 patients with HIV, three (10%) were co-infected with M. tuberculosis and P. jirovecii. No other causes of pneumonia were found in those three patients and CD4 cell counts less than 50 cell/mm(3) was reported.

Conclusions: The results of the current study showed a high rate of co-infection of M. tuberculosis and P. jirovecii in the Iranian patients with HIV. As the immune system condition worsened, the probability of occurrence of Pneumocystis Pneumonia (PCP) increased. Therefore, more specific, most rapid and sensitive tests should be utilized for diagnosis of PCP in this group of patients.
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http://dx.doi.org/10.5812/jjm.17254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376971PMC
February 2015

Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

PLoS One 2014 8;9(12):e114428. Epub 2014 Dec 8.

Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois, United States of America.

Introduction: While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran.

Material And Methods: A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations.

Results: Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%).

Conclusions: Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114428PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259318PMC
January 2016

Estimation of Recent Transmission of Mycobacterium Tuberculosis Strains among Iranian and Afghan Immigrants: A Cluster-Based Study.

J Clin Diagn Res 2014 Sep 20;8(9):DC05-8. Epub 2014 Sep 20.

Professor, Department of Microbiology, Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD),Shahid Beheshti University of Medical Sciences , Tehran, Iran .

Background: Iran has extended borders with high-TB burden countries (Afghanistan and Pakistan) and immigrations of these populations influences TB distribution in the region and threatens the control strategies. The aim of this study was to evaluate the extent of recent TB transmission among Iranian and Afghan cases.

Materials And Methods: Spoligotyping and 15-locus variable number tandem repeat (VNTR) typing were applied to genotype 102 MTB isolates (2009 to 2010). Phylogenetic relationships were analysed by two methods: a cluster-graph method and a minimum spanning tree (MST) method. Furthermore, evaluation of recent TB transmission was assessed with three indices including, RTIn, RTIn-1 and TMI.

Results: Using molecular typing, 35 different spoligotypes were detected among the studied isolates. Seventy seven cases (75.4%) were distributed into 10 clusters and the remaining 25 (24.5%) isolates had a unique pattern. The cluster sizes also ranged from 2 to 21 isolates. The most frequent spoligotype in our populations belong to Haarlem (n=30, 29.4%) followed by CAS (n= 29, 28.4%) and Beijing (n=16, 15.6%) lineages. The used indices give the following values: RTIn = 0.75, RTIn-1 = 0.65 and TMI = 0.24.

Conclusion: The low rate of TB transmission in our findings (24%) showed that the mode of TB transmission in Iran is mostly associated with reactivation of a previous TB infection and that recently a transmitted disease has a minor role. However, the increasing incidence of the intra-community transmission in recent years highlights the need for establishing new strategies for control of TB.
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http://dx.doi.org/10.7860/JCDR/2014/8886.4864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225883PMC
September 2014

Identification and genotyping of Mycobacterium tuberculosis isolated from water and soil samples of a metropolitan city.

Chest 2015 Apr;147(4):1094-1102

Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL. Electronic address:

Background: The potential role of environmental Mycobacterium tuberculosis in the epidemiology of TB remains unknown. We investigated the transmission of M tuberculosis from humans to the environment and the possible transmission of M tuberculosis from the environment to humans.

Methods: A total of 1,500 samples were collected from three counties of the Tehran, Iran metropolitan area from February 2012 to January 2014. A total of 700 water samples (47%) and 800 soil samples (53%) were collected. Spoligotyping and the mycobacterial interspersed repetitive units-variable number of tandem repeats typing method were performed on DNA extracted from single colonies. Genotypes of M tuberculosis strains isolated from the environment were compared with the genotypes obtained from 55 patients with confirmed pulmonary TB diagnosed during the study period in the same three counties.

Results: M tuberculosis was isolated from 11 of 800 soil samples (1%) and 71 of 700 water samples (10%). T family (56 of 82, 68%) followed by Delhi/CAS (11 of 82, 13.4%) were the most frequent M tuberculosis superfamilies in both water and soil samples. Overall, 27.7% of isolates in clusters were related. No related typing patterns were detected between soil, water, and clinical isolates. The most frequent superfamily of M tuberculosis in clinical isolates was Delhi/CAS (142, 30.3%) followed by NEW-1 (127, 27%). The bacilli in contaminated soil (36%) and damp water (8.4%) remained reculturable in some samples up to 9 months.

Conclusions: Although the dominant M tuberculosis superfamilies in soil and water did not correspond to the dominant M tuberculosis family in patients, the presence of circulating genotypes of M tuberculosis in soil and water highlight the risk of transmission.
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http://dx.doi.org/10.1378/chest.14-0960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388118PMC
April 2015