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Safari M, Tavakoli R, Aghasadeghi M, Tabatabaee Bafroee AS, Fateh A, Rahimi P. Study on the correlation between DPP9 rs2109069 and IFNAR2 rs2236757 polymorphisms with COVID-19 mortality. Nucleosides Nucleotides Nucleic Acids 2024:1-16. [PMID: 38660988 DOI: 10.1080/15257770.2024.2344179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Understanding the complex mechanisms of the immune system in dealing with the COVID-19 infection, which is probably related to the polymorphism in cytokine and chemokine genes, can explain the pro-inflammatory condition of patients. Therefore, in this study, the relationship between the frequency of single nucleotide polymorphisms in the two pro-inflammatory genes dipeptidylpeptidase 9 (DPP9) and interferon alpha and beta receptor subunit 2 (IFNAR2) and the severity of COVID-19 was assessed. This study involved 954 COVID-19 patients, including 528 recovered and 426 deceased patients. To investigate the polymorphisms of IFNAR2 rs2236757 and DPP9 rs2109069, we used the polymerase chain reaction with the restriction fragment length polymorphism assay. The results showed that IFNAR2 rs2236757 A allele is related to the reduced severity of the disease, whereas the incidence of DPP9 rs2109069 A allele was higher among the deceased than recovered individuals. On the other hand, in people carrying the G allele in the DPP9 gene polymorphism and the allele A in the IFNR2 gene polymorphism, the improvement of the disease was significantly higher. In conclusion, the results showed that IFNAR2 rs2236757 A allele is related to the decrease in the severity of the disease, while the frequency of DPP9 rs2109069 A allele was higher in deceased people than in recovered people. This shows the important role of genes related to inflammatory responses as well as the role of genetic variants of these genes in the severity of COVID-19.
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Affiliation(s)
- Mahnaz Safari
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Rezvan Tavakoli
- Department of Hepatitis and AIDS and Blood Transmitted Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammadreza Aghasadeghi
- Department of Hepatitis and AIDS and Blood Transmitted Diseases, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- Department of Hepatitis and AIDS and Blood Transmitted Diseases, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
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Madadi-Goli N, Ahmadi K, Kamakoli MK, Azizi M, Khanipour S, Dizaji SP, Nasehi M, Siadat SD, Fateh A, Vaziri F. The importance of heteroresistance and efflux pumps in bedaquiline-resistant Mycobacterium tuberculosis isolates from Iran. Ann Clin Microbiol Antimicrob 2024; 23:36. [PMID: 38664815 PMCID: PMC11046812 DOI: 10.1186/s12941-024-00694-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) continues to pose a threat to communities worldwide and remains a significant public health issue in several countries. We assessed the role of heteroresistance and efflux pumps in bedaquiline (BDQ)-resistant Mycobacterium tuberculosis isolates. METHODS Nineteen clinical isolates were included in the study, of which fifteen isolates were classified as MDR or XDR, while four isolates were fully susceptible. To evaluate BDQ heteroresistance, the Microplate Alamar Blue Assay (MABA) method was employed. For screening mixed infections, MIRU-VNTR was performed on clinical isolates. Mutations in the atpE and Rv0678 genes were determined based on next-generation sequencing data. Additionally, real-time PCR was applied to assess the expression of efflux pump genes in the absence and presence of verapamil (VP). RESULTS All 15 drug-resistant isolates displayed resistance to BDQ. Among the 19 total isolates, 21.05% (4/19) exhibited a heteroresistance pattern to BDQ. None of the isolates carried a mutation of the atpE and Rv0678 genes associated with BDQ resistance. Regarding the MIRU-VNTR analysis, most isolates (94.73%) showed the Beijing genotype. Fifteen (78.9%) isolates showed a significant reduction in BDQ MIC after VP treatment. The efflux pump genes of Rv0676c, Rv1258c, Rv1410c, Rv1634, Rv1819, Rv2459, Rv2846, and Rv3065 were overexpressed in the presence of BDQ. CONCLUSIONS Our results clearly demonstrated the crucial role of heteroresistance and efflux pumps in BDQ resistance. Additionally, we established a direct link between the Rv0676c gene and BDQ resistance. The inclusion of VP significantly reduced the MIC of BDQ in both drug-susceptible and drug-resistant clinical isolates.
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Affiliation(s)
- Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mahshid Nasehi
- Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- Center for Communicable Diseases Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, No. 358, 12th Farvardin Ave., Jomhoori St, Tehran, 1316943551, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Mofrad LZ, Fateh A, Sotoodehnejadnematalahi F, Asbi DNS, Davar Siadat S. The Effect of Akkermansia muciniphila and Its Outer Membrane Vesicles on MicroRNAs Expression of Inflammatory and Anti-inflammatory Pathways in Human Dendritic Cells. Probiotics Antimicrob Proteins 2024; 16:367-382. [PMID: 36884184 DOI: 10.1007/s12602-023-10058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Probiotics play a crucial role in immunomodulation by regulating dendritic cell (DC) maturation and inducing tolerogenic DCs. Akkermansia muciniphila affects inflammatory response by elevating inhibitory cytokines. We aimed to evaluate whether Akkermansia muciniphila and its outer membrane vesicles (OMVs) affect microRNA-155, microRNA-146a, microRNA-34a, and let-7i expression of inflammatory and anti-inflammatory pathways. Peripheral blood mononuclear cells (PBMCs) were isolated from the healthy volunteers. To produce DCs, monocytes were cultivated with granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4). DCs were allocated into six subgroups: DC + Lipopolysaccharide (LPS), DC + dexamethasone, DC + A. muciniphila (MOI 100, 50), DC + OMVs (50 µg/ml), and DC + PBS. The surface expression of human leukocyte antigen-antigen D related (HLA-DR), CD86, CD80, CD83, CD11c, and CD14 was examined using flow cytometry, and the expression of microRNAs was assessed using qRT-PCR, and the levels of IL-12 and IL-10 were measured using ELISA. A. muciniphila (MOIs 50, 100) could significantly decrease IL-12 levels relative to the LPS group. The IL-10 levels were decreased in the DC + LPS group than the DC + dexamethasone group. Treatment with A. muciniphila (MOI 100) and OMVs could elevate the concentrations of IL-10. DC treatment with LPS led to a significant increment in the expression of microRNA-155, microRNA-34a, and microRNA-146a. The expression of these microRNAs was reversed by A. muciniphilia and its OMVs treatment. Let-7i increased in treatment groups compared to the DC + LPS group. A. muciniphilia (MOI 50) had a substantial effect on the expression of HLA-DR, CD80, and CD83 on DCs. Therefore, DCs treatment with A. muciniphila led to induce tolerogenic DCs and the production of anti-inflammatory IL-10.
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Affiliation(s)
- Laya Zoghi Mofrad
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Ferdosnejad K, Zamani MS, Soroush E, Fateh A, Siadat SD, Tarashi S. Tuberculosis and lung cancer: metabolic pathways play a key role. Nucleosides Nucleotides Nucleic Acids 2024:1-20. [PMID: 38305273 DOI: 10.1080/15257770.2024.2308522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
Despite the fact that some cases of tuberculosis (TB) are undiagnosed and untreated, it remains a serious global public health issue. In the diagnosis, treatment, and control of latent and active TB, there may be a lack of effectiveness. An understanding of metabolic pathways can be fundamental to treat latent TB infection and active TB disease. Rather than targeting Mycobacterium tuberculosis, the control strategies aim to strengthen host responses to infection and reduce chronic inflammation by effectively enhancing host resistance to infection. The pathogenesis and progression of TB are linked to several metabolites and metabolic pathways, and they are potential targets for host-directed therapies. Additionally, metabolic pathways can contribute to the progression of lung cancer in patients with latent or active TB. A comprehensive metabolic pathway analysis is conducted to highlight lung cancer development in latent and active TB. The current study aimed to emphasize the association between metabolic pathways of tumor development in patients with latent and active TB. Health control programs around the world are compromised by TB and lung cancer due to their special epidemiological and clinical characteristics. Therefore, presenting the importance of lung cancer progression through metabolic pathways occurring upon TB infection can open new doors to improving control of TB infection and active TB disease while stressing that further evaluations are required to uncover this correlation.
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Affiliation(s)
| | | | - Erfan Soroush
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Tarashi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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5
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Sadeghi Mofrad S, Boozarjomehri Amnieh S, Pakzad MR, Zardadi M, Ghazanfari Jajin M, Anvari E, Moghaddam S, Fateh A. The death rate of COVID-19 infection in different SARS-CoV-2 variants was related to C-reactive protein gene polymorphisms. Sci Rep 2024; 14:703. [PMID: 38184750 PMCID: PMC10771501 DOI: 10.1038/s41598-024-51422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/04/2024] [Indexed: 01/08/2024] Open
Abstract
The serum level of C-reactive protein (CRP) is a significant independent risk factor for Coronavirus disease 2019 (COVID-19). A link was found between serum CRP and genetic diversity within the CRP gene in earlier research. This study examined whether CRP rs1205 and rs1800947 polymorphisms were associated with COVID-19 mortality among various severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) variants. We genotyped CRP rs1205 and rs1800947 polymorphisms in 2023 deceased and 2307 recovered patients using the polymerase chain reaction-restriction fragment length polymorphism method. There was a significant difference between the recovered and the deceased patients in terms of the minor allele frequency of CRP rs1205 T and rs1800947 G. In all three variants, COVID-19 mortality rates were associated with CRP rs1800947 GG genotype. Furthermore, CRP rs1205 CC and rs1800947 GG genotypes showed higher CRP levels. It was found that the G-T haplotype was prevalent in all SARS-CoV-2 variants. The C-C and C-T haplotypes were statistically significant in Delta and Omicron BA.5 variants, respectively. In conclusion, polymorphisms within the CRP gene may relate to serum CRP levels and mortality among COVID-19 patients. In order to verify the utility of CRP polymorphism correlation in predicting COVID-19 mortality, a replication of these results is needed.
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Affiliation(s)
- Sahar Sadeghi Mofrad
- Department of Microbiology, Islamic Azad University of Central Tehran Branch, Tehran, Iran
| | | | - Mohammad Reza Pakzad
- Faculty of Veterinary Medicine, Tabriz Medical Science Branch, Islamic Azad University, Tabriz, Iran
| | - Mina Zardadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran
| | - Sina Moghaddam
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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6
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Yari S, Afrough P, Yari F, Ghazanfari Jajin M, Fateh A, Hadizadeh Tasbiti A. A potent subset of Mycobacterium tuberculosis glycoproteins as relevant candidates for vaccine and therapeutic target. Sci Rep 2023; 13:22194. [PMID: 38092899 PMCID: PMC10719292 DOI: 10.1038/s41598-023-49665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Tuberculosis (TB) remains one of the most afflictive bacterial infections globally. In high burden TB countries, surveillance, diagnosis and treatment of drug resistant TB (RR and X/MDRTB) display a crucial public health challenge. Therefore, we need new TB vaccines; diagnostic and therapeutic strategies to briskly prevent disease promotion; reduce drug-resistant TB and protect everyone from disease. The study identified various potent membrane and cell wall M. tuberculosis glycolipoproteins that are relevant for diagnostics, drug and vaccine discovery. A M. tuberculosis Proskauer and Beck broth culture was extracted for total proteins by ammonium sulfate method. After ConA-Affinity Chromatography reputed glycoproteins were collected followed by 2DE gel electrophoresis and LC Mass spectrometry. A total of 293 glycoproteins were identified using GlycoPP and IEDB database. Probable conserved trans-membrane protein (Rv0954), LpqN (Rv0583), PPE68 (Rv3873), Phosphate-binding protein (Rv0932c), PPE61 (Rv3532) and LprA (Rv1270c), had the highest glycosylation percentage value with 13.86%, 11.84%, 11.68%, 11.1%, 10.59% and10.2%, respectively. Our study discloses several dominant glycoproteins that play roles in M. tuberculosis survival, and immunogenicity. These include glycoproteins involved in antigenicity, transport and biosynthesis of M. tuberculosis cell envelope, pathogen-host interaction and drug efflux pumps, which are considered as a feasible drug targets or TB new vaccine candidates.
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Affiliation(s)
- Shamsi Yari
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Parviz Afrough
- Hepatitis Research Center, Shahid Rahimi Hospital, Aligoudarz School of Nursing, Lorestan University of Medical Science, Khorramabad, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion, Tehran, Iran
| | - Morteza Ghazanfari Jajin
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Abolfazl Fateh
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran
| | - Alireza Hadizadeh Tasbiti
- TB Protein Chemistry Lab, Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Pasteur Ave, Tehran, 13164, Iran.
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Moghaddam N, Goodarzi MT, Moghaddam S, Sakhaee F, Ahmadi I, Anvari E, Fateh A. Relationship Between Human FCγ RIIA rs1801274 G Allele and Risk of Death Among Different SARS-CoV-2 Variants. Viral Immunol 2023; 36:678-685. [PMID: 38029355 DOI: 10.1089/vim.2023.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in late 2019 and spread very quickly across the world. Different responses to infections have been related to fragment crystallizable gamma-receptor II alpha (FcγRIIA) polymorphisms. The purpose of this investigation was to determine if FCγRIIA rs1801274 polymorphism was related to COVID-19 mortality among different variants of SARS-CoV-2. The FCγRIIA rs1801274 polymorphism was genotyped using the polymerase chain reaction-restriction fragment length polymorphism technique in 1,734 recovered and 1,450 deceased patients. Deceased patients had significantly higher minor allele frequency of the FCγRIIA rs1801274 G allele than in the recovered cases. The COVID-19 mortality was associated with FCγRIIA rs1801274 GG and AG genotypes in the Delta variant and with FCγRIIA rs1801274 GG genotypes in the Alpha and Omicron BA.5 variants. The reverse transcription-quantitative polymerase chain reaction Ct values revealed statistically significant differences between individuals with a G allele and those with an A allele. In conclusion, among the several SARS-CoV-2 variants, there may be a correlation between the mortality rate of COVID-19 and the G allele of FCγRIIA rs1801274. To confirm our findings, thorough research is still required.
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Affiliation(s)
- Nazanin Moghaddam
- Department of Biochemistry, Shahrood Branch, Islamic Azad University, Shahrood, Iran
| | | | - Sina Moghaddam
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Nedaei F, Esmaeili Rastaghi AR, Goodarzi E, Haji Mullah Asadullah H, Mirhadi F, Fateh A. Introduction and effect of natural selection analysis at common mutations of SARS-CoV-2 spike gene in Iran. Virus Res 2023; 336:199202. [PMID: 37595664 PMCID: PMC10491845 DOI: 10.1016/j.virusres.2023.199202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The epidemic of coronavirus disease 2019 (COVID-19) was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of SARS-Cov-2 is composed of two subunits, S1 and S2. This study aimed to describe SARS-CoV-2 haplotypes in Iranians based on the S gene, which plays a key role in the receptor recognition and cell membrane fusion proses. 95 positive saliva samples for SARS-CoV-2 were amplified and sequenced for the S gene. The sequences were classified into 35 haplotypes, which 11 haplotypes were new (H1, H2, H3, H4, H6, H7, H11, H13, H15, H16, H25) and have not been reported so far. Amino acid substitutions were found at 40 positions that 23 were located at S1 subunit and 16 were at S2 subunit and one was at cleavage loop (P681H/R), thus polymorphisms at S1 subunit were found to be higher than S2. The neutrality index (NI) analyses showed a negative departure from the neutral substitution patterns (NI > 1) for S1 and S2 subunit in the studied sequences. The co-occurrence of B-cell epitopes and mutation sites were found in seven positions with more probably to be exposed the immune system pressure. In conclusion, the results provide the significant data to design an effective vaccine based on this protein.
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Affiliation(s)
- Fatemeh Nedaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Esmaeil Goodarzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Fatemeh Mirhadi
- Department of Medical science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Al-Mohammedawi AKK, Anvari E, Fateh A. Relationship between CDX2 rs11568820 and EcoRV rs4516035 polymorphisms on the vitamin D receptor gene with susceptibility to different SARS-CoV-2 variants. Cell Biol Int 2023; 47:1728-1736. [PMID: 37369952 DOI: 10.1002/cbin.12064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023]
Abstract
Several studies have revealed that vitamin D deficiency is linked to an increased risk of developing coronavirus disease 19 (COVID-19). In individuals with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, vitamin D receptor activation is required to decrease acute respiratory distress syndrome. The purpose of this study was to examine the genotypic distribution and allelic frequencies of CDX2 rs11568820 and EcoRV rs4516035 polymorphisms in COVID-19 patients with various SARS-CoV-2 variants. For genotyping of CDX2 rs11568820 and EcoRV rs4516035 polymorphisms, we used the polymerase chain reaction-restriction fragment length polymorphism technique in 1734 and 1450 recovered and deceased patients, respectively. The results indicated the rate of COVID-19 mortality was associated with CDX2 rs11568820 AA and GA genotypes in the Delta variant and with CDX2 rs11568820 AA in the Omicron BA.5 variant, while no association was shown in the Alpha variant. Therefore, the rate of COVID-19 mortality was associated with EcoRV rs4516035 TC and CC genotypes in the Delta variant, while no association was shown in the Alpha and Omicron BA.5 variants. According to our analysis, the T-G haplotype was more common in all SARS-CoV-2 variants. The C-A haplotype was associated with COVID-19 mortality in the Delta and Omicron BA.5 variants, and the T-A haplotype was related to the Alpha variant. In conclusion, the genotype frequencies of the CDX2 rs11568820 and EcoRV rs4516035 polymorphisms between SARS-CoV-2 variants were significantly different between the deceased patients and recovered patients. However, more studies should be done to confirm the results.
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Affiliation(s)
| | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Yaghoubfar R, Zare BanadKoki E, Ashrafian F, Shahryari A, Kariman A, Davari M, Fateh A, Khatami S, Siadat SD. The impact of Akkermansia muciniphila and its extracellular vesicles in the regulation of serotonergic gene expression in a small intestine of mice. Anaerobe 2023; 83:102786. [PMID: 37797929 DOI: 10.1016/j.anaerobe.2023.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
OBJECTIVES A better understanding of host-microbe interactions as a cross-talk between the gastrointestinal (GI) tract and the gut microbiota can help treat and prevent GI disorders by improving the maintenance of GI homeostasis. The gut microbiota can affect signaling molecules, such as serotonin, which regulates endocrine systems through the GI tract. Moreover, studying the effects of gut microbiota in the small intestine on the human GI tract health is pivotal. METHODS Male C57BL/6J mice (n = 30, 10 mice per group) were orally gavaged with 200 μL of PBS (control group); mice in group II were orally gavaged with 109 colony-forming units (CFU)/200 μL of viable A. muciniphila, suspended in PBS (A. muciniphila group); and mice in group III were orally gavaged with 10 μg of protein/200 μL of EVs (A. muciniphila-EV group) once daily for four weeks. The gene expression of serotonin system-related genes (Slc6a4, Tph1, Mao, Htr3, Htr4, and Htr7) was examined by quantitative real-time PCR (qPCR) method. RESULTS Based on the results, A. muciniphila significantly affected the mRNA expression of genes related to the serotonin system (Tph1, Mao, Htr3B, and Htr7) in the duodenum and (Htr3B, Htr4 and Htr7) in the ileum of mice (P < 0.05). Moreover, A. muciniphila-derived EVs affected the expression of major genes related to the serotonin system (Tph1, slc6a4a, Mao, Htr3B, Htr4, and Htr7) in the duodenum and ileum of mice (P < 0.05). CONCLUSIONS The present findings may pave the way for further investigation of the effects of strain-specific probiotics on the serotonergic system, which is currently in its infancy.
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Affiliation(s)
- Rezvan Yaghoubfar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Ashrafian
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Arefeh Shahryari
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Mehdi Davari
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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11
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Nour Neamatollahi A, Tarashi S, Ebrahimzadeh N, Vaziri F, Zaheri Birgani MA, Aghasadeghi M, Fateh A, Siadat SD, Bouzari S. Evaluation of miR-let-7f, miR-125a, and miR-125b expression levels in sputum and serum samples of Iranians and Afghans with pulmonary tuberculosis. Iran J Microbiol 2023; 15:665-673. [PMID: 37941875 PMCID: PMC10628080 DOI: 10.18502/ijm.v15i5.13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Background and Objectives The role of microRNAs (miRNAs) in tuberculosis infection is well established. As microRNAs are able to change expression profiles according to different conditions, they can be useful biomarkers. Iranians and Afghans with tuberculosis were studied for three immune-related miRNAs (miR-let-7f, miR-125a, and miR-125b). Materials and Methods A total of 60 Iranian and Afghan patients with active pulmonary TB were enrolled in the Pulmonary Department of the Pasteur Institute of Iran. Serum and sputum samples were collected simultaneously from all participants. A Real-time PCR was conducted to detect differentially expressed miRNAs. Results Iranian (P<0.0001) and Afghan (P<0.0001) serum samples and Afghan (P<0.0001) sputum samples overexpressed miR-125a, whereas Iranian sputum samples showed downregulation (P=0.0039). In both Iranian (P<0.0001; P=0.0007) and Afghan (P<0.0001; P<0.0001) serum and sputum samples, miR-125b was overexpressed. Furthermore, miR-let-7f down-regulation was observed in serum and sputum samples (P<0.0001), whereas Iranian sputum samples had no statistically significant differences (P=0.348). Conclusion Overexpression of miR-125a and miR-125b has been detected in Iranian and Afghan samples. In both races, miR-let-7f downregulation has been confirmed. Identification of miRNA profiles under different conditions opens the door to evaluating potential new biomarkers for diagnosis, disease monitoring, and therapeutic markers in TB infection.
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Affiliation(s)
- Ali Nour Neamatollahi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Mohammadreza Aghasadeghi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Bouzari
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
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12
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Meskini M, Madadi N, Ahmadi K, Vaziri F, Fateh A, Siadat SD. Tuberculosis prevention, diagnosis, and treatment financial profile during 2006-2021: PART A. Cost Eff Resour Alloc 2023; 21:68. [PMID: 37726829 PMCID: PMC10507895 DOI: 10.1186/s12962-023-00479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) is a communicable disease that is a major cause of death and one of the leading causes of death worldwide. Currently, there is no analyzed data to examine the financial profile of TB by country, continent, and year; this article analyzed TB prevention, diagnosis, and treatment financial profile during the last two decades. METHODS Original research, reviews, and governmental databases are analyzed to present the financial profile of TB. RESULTS Analyzed data showed Europe (23137.133), Asia (20137.073), and Africa (15237.973) had the most allocated funds (US $ million), and Oceania (236.702), and America (4745.043) had the lowest allocated fund (US $ million) during 2006-2021. Additionally, the allocation of funds (domestic funds, global funds, and grants [excluding global funds]) in different countries and proper planning for TB eradication has caused that in the last two decades, the slope of the confirmed cases and deaths graph line is negative. CONCLUSION The number of confirmed cases and deaths reported globally is decreasing. The trend lines showed that the assigned funds are increasing, indicating that the TB eradication plan can be apprehended soon.
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Affiliation(s)
- Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Nahid Madadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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13
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Sheikhian F, Sadeghi Mofrad S, Tarashi S, Ghazanfari Jajin M, Sakhaee F, Ahmadi I, Anvari E, Sheikhpour M, Fateh A. The impact of ACE2 polymorphisms (rs1978124, rs2285666, and rs2074192) and ACE1 rs1799752 in the mortality rate of COVID-19 in different SARS-CoV-2 variants. Hum Genomics 2023; 17:54. [PMID: 37328914 DOI: 10.1186/s40246-023-00501-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Clinical severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outcomes could be influenced by genetic polymorphisms in angiotensin I-converting enzyme (ACE1) and ACE2. This study aims to examine three polymorphisms (rs1978124, rs2285666, and rs2074192) on the ACE2 gene and ACE1 rs1799752 (I/D) in patients who have coronavirus disease 2019 (COVID-19) with various SARS-CoV-2 variants. METHODS Based on polymerase chain reaction-based genotyping, four polymorphisms in the ACE1 and ACE2 genes have been identified in 2023 deceased patients and 2307 recovered patients. RESULTS The ACE2 rs2074192 TT genotype was associated with the COVID-19 mortality in all three variants, whereas the CT genotype was associated with the Omicron BA.5 and Delta variants. ACE2 rs1978124 TC genotypes were related to COVID-19 mortality in the Omicron BA.5 and Alpha variants, but TT genotypes were related to COVID-19 mortality in the Delta variant. It was found that ACE2 rs2285666 CC genotypes were associated with COVID-19 mortality in Delta and Alpha variants, and CT genotypes in Delta variants. There was an association between ACE1 rs1799752 DD and ID genotypes in the Delta variant and COVID-19 mortality, whereas there was no association in the Alpha or Omicron BA.5 variants. In all variants of SARS-CoV-2, CDCT and TDCT haplotypes were more common. In Omicron BA.5 and Delta, CDCC and TDCC haplotypes were linked with COVID-19 mortality. In addition to COVID-19 mortality, the CICT, TICT, and TICC were significantly correlated. CONCLUSION The ACE1/ACE2 polymorphisms had an impact on COVID-19 infection, and these polymorphisms had different effects in various SARS-CoV-2 variants. To confirm these results, however, more research needs to be conducted.
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Affiliation(s)
- Farzaneh Sheikhian
- Department of Biology, Parand Branch, Islamic Azad University, Parand, Iran
| | - Sahar Sadeghi Mofrad
- Department of Microbiology, Islamic Azad University of Central Tehran Branch, Tehran, Iran
| | - Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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14
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Gholami M, Sakhaee F, Mirzaei Gheinari F, Sotoodehnejadnematalahi F, Ghazanfari Jajin M, Zamani MS, Ahmadi I, Anvari E, Fateh A. Interferon-Induced Transmembrane Protein 3 rs34481144 C/T Genotype and Clinical Parameters Related to Progression of COVID-19. J Immunol Res 2023; 2023:2345062. [PMID: 37323564 PMCID: PMC10266908 DOI: 10.1155/2023/2345062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Recent research has associated the interferon-induced transmembrane protein 3 gene (IFITM3) with the outcomes of coronavirus disease 2019 (COVID-19), although the findings are contradictory. This study aimed to determine the relationship between IFITM3 gene rs34481144 polymorphism and clinical parameters with COVID-19 mortality. The tetra-primer amplification refractory mutation system-polymerase chain reaction assay was used to analyze IFITM3 rs34481144 polymorphism in 1,149 deceased and 1,342 recovered patients. The clinical parameters were extracted from the patients' medical records. In this study, the frequency of IFITM3 rs34481144 CT genotypes (OR 1.47, 95% CI 1.23-1.76, P < 0.0001) in both sexes was significantly higher in deceased patients than in recovered patients. Moreover, IFITM3 rs34481144 TT genotypes (OR 3.38, 95% CI 1.05-10.87, P < 0.0001) in women were significantly associated with COVID-19 mortality. The multivariable logistic regression model results indicated that mean age (P < 0.001), alkaline phosphatase (P = 0.005), alanine aminotransferase (P < 0.001), low-density lipoprotein (P < 0.001), high-density lipoprotein (P < 0.001), fasting blood glucose (P = 0.010), creatinine (P < 0.001), uric acid (P < 0.001), C-reactive protein (P = 0.004), 25-hydroxyvitamin D (P < 0.001), erythrocyte sedimentation rate (P < 0.001), and real-time PCR Ct values (P < 0.001) were linked with increased COVID-19 death rates. In conclusion, IFITM3 rs34481144 gene polymorphism was linked to the mortality of COVID-19, with the rs34481144-T allele being especially important for mortality. Further studies are needed to confirm the results of this study.
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Affiliation(s)
- Melika Gholami
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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15
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Tavakoli R, Rahimi P, Hamidi-Fard M, Eybpoosh S, Doroud D, Ahmadi I, Anvari E, Aghasadeghi M, Fateh A. Expression of TRIM56 gene in SARS-CoV-2 variants and its relationship with progression of COVID-19. Future Virol 2023; 18:563-574. [PMID: 38051999 PMCID: PMC10348059 DOI: 10.2217/fvl-2022-0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/19/2023] [Indexed: 10/13/2023]
Abstract
Aim The present study aimed to determine a correlation between differential TRIM56 expression levels and severe infections of COVID-19 between the Alpha, Delta and Omicron BA.5 variants. Materials & methods This study was performed on 330 COVID-19 patients, including 142 with severe and 188 with mild infections, as well as 160 healthy controls. The levels of TRIM56 gene expression were determined using a qPCR. Results TRIM56 gene showed significantly lower mRNA expression in the severe and mild groups compared with healthy individuals. Our finding indicated the high and low reduction of TRIM56 mRNA expression in Delta and Omicron BA.5 variant, respectively. Conclusion Further research is needed to characterize the impact of TRIM proteins on the severity of COVID-19.
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Affiliation(s)
- Rezvan Tavakoli
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology & Biostatistics, Research Centre for Emerging & Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- Quality Control Department, Production & Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Mohammadreza Aghasadeghi
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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16
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Tarashi S, Sakhaee F, Masoumi M, Ghazanfari Jajin M, Siadat SD, Fateh A. Molecular epidemiology of nontuberculous mycobacteria isolated from tuberculosis-suspected patients. AMB Express 2023; 13:49. [PMID: 37202495 DOI: 10.1186/s13568-023-01557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/09/2023] [Indexed: 05/20/2023] Open
Abstract
It is a growing problem around the world to deal with nontuberculous mycobacteria infection (NTM), but its clinical significance is still largely unknown. This study aims to investigate the epidemiology of NTM infections from various clinical samples and determine their clinical significance. From December 2020 to December 2021, 6125 clinical samples were collected. In addition to phenotypic detection, genotypic detection through multilocus sequence typing (hsp65, rpoB, and 16S rDNA genes) and sequencing was also conducted. Records of patients were consulted for clinical information, such as symptoms and radiological findings. Of the 6,125 patients, 351 (5.7%) were positive for acid-fast bacteria (AFB). Out of 351 AFB, 289 (82.3%) and 62 (17.7%) subjects were identified as M. tuberculosis complex (MTC) and NTM strains, respectively. Isolates of Mycobacterium simiae and M. fortuitum were the most frequent, followed by isolates of M. kansasii and M. marinum. We also isolated M. chelonae, M. canariasense, and M. jacuzzii, which are rarely reported. Symptoms (P = 0.048), radiographic findings (P = 0.013), and gender (P = 0.039) were associated with NTM isolates. M. Fortuitum, M. simiae, and M. kansasii presented with bronchiectasis, infiltration, and cavitary lesions most frequently, while cough was the most common symptom. In conclusion, Mycobacterium simiae and M. fortuitum were presented in seventeen and twelve NTM isolates from the collected samples. There is evidence that NTM infections in endemic settings may contribute to the dissemination of various diseases and the control of tuberculosis. In spite of this, further research is needed to evaluate the clinical significance of NTM isolates.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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17
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Al-Gharrawi ANR, Anvari E, Fateh A. Association of ApaI rs7975232 and BsmI rs1544410 in clinical outcomes of COVID-19 patients according to different SARS-CoV-2 variants. Sci Rep 2023; 13:3612. [PMID: 36869206 PMCID: PMC9983525 DOI: 10.1038/s41598-023-30859-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/02/2023] [Indexed: 03/05/2023] Open
Abstract
A growing body of research has shown how important vitamin D is in the prognosis of coronavirus disease 19 (COVID-19). The vitamin D receptor is necessary for vitamin D to perform its effects, and its polymorphisms can help in this regard. Therefore, we aimed to evaluate whether the association of ApaI rs7975232 and BsmI rs1544410 polymorphisms in different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were influential in the outcomes of COVID-19. The polymerase chain reaction-restriction fragment length polymorphism method was utilized to determine the different genotypes of ApaI rs7975232 and BsmI rs1544410 in 1734 and 1450 patients who had recovered and deceased, respectively. Our finding revealed that the ApaI rs7975232 AA genotype in the Delta and Omicron BA.5 and the CA genotype in the Delta and Alpha variants were associated with higher mortality rate. Also, the BsmI rs1544410 GG genotype in the Delta and Omicron BA.5 and the GA genotype in the Delta and Alpha variants were related to a higher mortality rate. The A-G haplotype was linked with COVID-19 mortality in both the Alpha and Delta variants. The A-A haplotype for the Omicron BA.5 variants was statistically significant. In conclusion, our research revealed a connection between SARS-CoV-2 variants and the impacts of ApaI rs7975232 and BsmI rs1544410 polymorphisms. However, more research is still needed to substantiate our findings.
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Affiliation(s)
| | - Enayat Anvari
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Science, Ilam, Iran.
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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18
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Tavakoli R, Rahimi P, Hamidi-Fard M, Eybpoosh S, Doroud D, Sadeghi SA, Zaheri Birgani M, Aghasadeghi M, Fateh A. Impact of TRIM5α and TRIM22 Genes Expression on the Clinical Course of Coronavirus Disease 2019. Arch Med Res 2023; 54:105-112. [PMID: 36621405 PMCID: PMC9794484 DOI: 10.1016/j.arcmed.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The innate immune response in humans involves a wide variety of factors, including the tripartite motif-containing 5α (TRIM5α) and 22 (TRIM22) as a cluster of genes on chromosome 11 that have exhibited antiviral activity in several viral infections. We analyzed the correlation of the expression of TRIM5α and TRIM22 with the severity of Coronavirus Disease 2019 (COVID-19) in blood samples of 330 patients, divided into two groups of severe and mild disease, versus the healthy individuals who never had contact with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). METHODS The transcription level of TRIM5α and TRIM22 was determined by quantitative real-time polymerase chain reaction (qPCR). The laboratory values were collected from the patients' records. RESULTS The expression of both genes was significantly lower in the severe group containing the hospitalized patients than in both the mild group and the control group. However, in the mild group, TRIM22 expression was significantly higher (p <0.0001) than in the control group while TRIM5α expression was not significantly different between these two groups. We found a relationship between the cycle threshold (Ct) value of patients and the expression of the aforementioned genes. CONCLUSION The results of our study indicated that lower Ct values or higher RNA viral load might be associated with the downregulation of TRIM5α and TRIM22 and the severity of COVID-19. Additional studies are needed to confirm the results of this study.
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Affiliation(s)
- Rezvan Tavakoli
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- Quality Control Department, Production and Research Complex, Pasteur institute of Iran, Tehran, Iran
| | | | | | - Mohammadreza Aghasadeghi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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19
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Albu-Mohammed WHM, Anvari E, Fateh A. Evaluating the Role of BglI rs739837 and TaqI rs731236 Polymorphisms in Vitamin D Receptor with SARS-CoV-2 Variants Mortality Rate. Genes (Basel) 2022; 13:genes13122346. [PMID: 36553614 PMCID: PMC9777972 DOI: 10.3390/genes13122346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
A lack of vitamin D is a potential risk factor for coronavirus disease (COVID-19). Variants in the Vitamin D Receptor (VDR) gene, such as BglI rs739837 and TaqI rs731236, are associated with various viral infection progressions. This study aimed to evaluate the relationship between the BglI rs739837 and TaqI rs731236 polymorphisms and the mortality rate of COVID-19 based on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. The genotyping of BglI rs739837 and TaqI rs731236 genotypes was analyzed using the polymerase chain reaction-restriction fragment length polymorphism in 1734 improved and 1450 deceased patients positive for SARS-CoV-2. In this study, the rate of COVID-19 mortality was correlated with TaqI rs731236 TC and CC in the α variant and with TaqI rs731236 CC in the Delta variant, whereas no relationship was found in the Omicron BA.5 variant. In addition, the rate of COVID-19 mortality was associated with BglI rs739837 GT and TT in the Omicron BA.5 variant, while there was no association between BglI rs739837 and COVID-19 mortality in the α and Delta variants. The TG haplotype was more common in all SARS-CoV-2 variants, while the CT haplotype was associated with COVID-19 mortality in the Delta and Omicron BA.5 variants. In conclusion, this study indicated that the impacts of BglI rs739837 and TaqI rs731236 polymorphisms were related to SARS-CoV-2 variants. However, further research is still needed to approve our findings.
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Affiliation(s)
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam 693917134, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran 1316943551, Iran
- Correspondence: ; Tel.: +98-216-411-2282; Fax: +98-216-411-2213
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20
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Tarharoudi R, Sari S, Sakhaee F, Vaziri F, Rahimi Jamnani F, Siadat SD, Fateh A. BK polyomavirus in Iranian patients with papillary thyroid cancer: Is it a major future challenge? J Med Virol 2022; 94:6023-6027. [PMID: 35927225 DOI: 10.1002/jmv.28047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 01/06/2023]
Abstract
BK polyomavirus (BKPyV) is a well-known cause of nephropathy in renal transplant recipients. It has recently received much attention from researchers as a major predisposing factor for various cancers. This study aimed to investigate how BKPyV affected the advancement of papillary thyroid carcinoma (PTC). A total of 1057 samples were tested for BKPyV DNA and RNA, comprising 645 paraffin-embedded PTC biopsy samples (PEBS), 412 fresh biopsy samples (FBS), and 1057 adjacent noncancerous samples. The BKPyV DNA was found in 511 (48.3%) of the specimens, including 347 (84.2%) FBS and 164 (25.4%) PEBS. The mean BKPyV copy number was significantly lower in patients with PEBS (0.5 × 10-4 ± 0.1 × 10-4 copies/cell) than in FBS (1.3 × 10-1 ± 0.2 × 10-1 copies/cell) and non-PTC normal samples (0.3 × 10-5 ± 0.04 × 10-5 copies/cell). The PEBS had lower LT-Ag RNA expression than FBS, and no VP1 gene transcript expression was detected. In conclusion, although our findings indicated the presence of BKPyV in some Iranian PTC patients, more research is needed to corroborate these findings.
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Affiliation(s)
- Rahil Tarharoudi
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soyar Sari
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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21
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Beheshti Shirazi SS, Sakhaee F, Sotoodehnejadnematalahi F, Zamani MS, Ahmadi I, Anvari E, Fateh A. rs12329760 Polymorphism in Transmembrane Serine Protease 2 Gene and Risk of Coronavirus Disease 2019 Mortality. Biomed Res Int 2022; 2022:7841969. [PMID: 36457338 PMCID: PMC9708353 DOI: 10.1155/2022/7841969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/04/2022] [Accepted: 11/12/2022] [Indexed: 08/29/2023]
Abstract
The protease produced by the transmembrane serine protease 2 (TMPRSS2) gene enhances viral infections and has been linked to severe acute respiratory syndrome coronavirus 2 pathogenesis. Therefore, this study evaluated the association between TMPRSS2 and coronavirus disease 2019 (COVID-19) mortality. TMPRSS2 rs12329760 polymorphism was genotyped using the tetraprimer amplification refractory mutation system-polymerase chain reaction method in 592 dead and 693 improved patients. In the current study, the frequency of TMPRSS2 rs12329760 CC than TT genotypes was significantly lower in improved patients than in dead patients. According to the findings of the multivariate logistic regression test, higher levels of mean age, creatinine, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, lower levels of 25-hydroxyvitamin D, uric acid, and real-time PCR Ct values and TMPRSS2 rs12329760 CC genotype were observed to be associated with increased COVID-19 mortality rates. In conclusion, the TMPRSS2 rs12329760 CC genotype was a polymorphism linked to a significantly higher incidence of severe COVID-19. Further studies are required to corroborate the obtained findings.
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Affiliation(s)
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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22
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Gholami M, Sakhaee F, Sotoodehnejadnematalahi F, Zamani MS, Ahmadi I, Anvari E, Fateh A. Increased risk of COVID-19 mortality rate in IFITM3 rs6598045 G allele carriers infected by SARS-CoV-2 delta variant. Hum Genomics 2022; 16:60. [PMID: 36403064 PMCID: PMC9675951 DOI: 10.1186/s40246-022-00434-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The interferon-induced transmembrane-protein 3 (IFITM3) is a vital component of the immune system's defense against viral infection. Variants in the IFITM3 gene have been linked to changes in expression and the risk of severe Coronavirus disease 2019 (COVID-19). This study aimed to investigate whether IFITM3 rs6598045, quantitative polymerase chain reaction (qPCR) cycle threshold (Ct) values, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are associated with an increased mortality rate of COVID-19. METHODS The genotyping of IFITM3 rs6598045 polymorphism was analyzed using the amplification refractory mutation system-polymerase chain reaction in 1342 recovered and 1149 deceased patients positive for SARS-CoV-2. RESULTS In this study, IFITM3 rs6598045 G allele as minor allele frequency was significantly more common in the deceased patients than in the recovered ones. Furthermore, the highest mortality rates were observed in Delta variant and lowest qPCR Ct values. COVID-19 mortality was associated with IFITM3 rs6598045 GG and AG in Delta variant and IFITM3 rs6598045 AG in Alpha variant. A statistically significant difference was observed in the qPCR Ct values between individuals with GG and AG genotypes and those with an AA genotype. CONCLUSION A possible correlation was observed between the mortality rate of COVID-19, the G allele of IFITM3 rs6598045, and SARS-CoV-2 variants. However, large-scale research is still required to validate our results.
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Affiliation(s)
- Melika Gholami
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran ,grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fattah Sotoodehnejadnematalahi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Saber Zamani
- grid.412501.30000 0000 8877 1424Immunoregulation Research Center, Shahed University, Tehran, Iran
| | - Iraj Ahmadi
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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23
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Masoumi M, Sakhaee F, Zolfaghari MR, Tarashi S, Rahimi Jamnani F, Vaziri F, Siadat SD, Fateh A. Mixed pulmonary infection with four isolates of nontuberculous mycobacteria: a case report of mycobacterium bacteremicum infection. Pneumonia (Nathan) 2022; 14:7. [PMCID: PMC9636635 DOI: 10.1186/s41479-022-00100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
Background
A mixed pulmonary infection of Mycobacterium bacteremicum and three different isolates of nontuberculous mycobacteria (NTM) is an unusual clinical manifestation and have not yet been indicated. In this case report, we reported four isolates of NTM using phenotypic and genotypic test of pulmonary sample in Tehran, Iran.
Case presentation
We report a case of severe pulmonary disease in a 19-year-old male patient with productive cough, shortness of breath, and low-grade fever for several weeks. The C-reactive protein (CRP) level (80.2 mg/L) and erythrocyte sedimentation rate (ESR) (95 mm/h) were high. The computed tomographic scan indicated bronchiectasis, nodular opacities, consolidation, and cavitary lesions on both sides. The result of purified protein derivative (PPD) test was equal to 15 mm. The sequences of hsp65, rpoB, and 16S rDNA genes indicated more than 99% homology to four isolates of nontuberculous mycobacteria (NTM), including Mycobacterium fortuitum, M. chelonae, M. mucogenicum, and M. bacteremicum. We found that all four strains were susceptible to amikacin, cefoxitin, ciprofloxacin, clarithromycin, imipenem, and linezolid. The patient was treated with ciprofloxacin, clarithromycin, and amikacin, along with Montelukast, for five months.
Conclusion
We report a case of severe pulmonary infection by four isolates of NTM. After treatment, the patient reported complete resolution of the signs and a weight gain of 5 kg; also, the CRP and ESR were normal. Nine months after the infection diagnosis, a new CT scan revealed further improvements.
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24
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Tavakoli R, Rahimi P, Hamidi-Fard M, Eybpoosh S, Doroud D, Ahmadi I, Anvari E, Aghasadeghi M, Fateh A. Correction: comparing the expression levels of tripartite motif containing 28 in mild and severe COVID-19 infection. Virol J 2022; 19:171. [PMID: 36316685 PMCID: PMC9624030 DOI: 10.1186/s12985-022-01903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Rezvan Tavakoli
- grid.420169.80000 0000 9562 2611Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- grid.420169.80000 0000 9562 2611Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- grid.420169.80000 0000 9562 2611Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- grid.420169.80000 0000 9562 2611Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- grid.420169.80000 0000 9562 2611Quality Control Department, Production and Research Complex, Pasteur institute of Iran, Tehran, Iran
| | - Iraj Ahmadi
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- grid.449129.30000 0004 0611 9408Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Mohammadreza Aghasadeghi
- grid.420169.80000 0000 9562 2611Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- grid.420169.80000 0000 9562 2611Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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25
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Moghaddam S, Nojoomi F, Dabbagh Moghaddam A, Mohammadimehr M, Sakhaee F, Masoumi M, Siadat SD, Fateh A. Isolation of nontuberculous mycobacteria species from different water sources: a study of six hospitals in Tehran, Iran. BMC Microbiol 2022; 22:261. [PMID: 36309645 DOI: 10.1186/s12866-022-02674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Nontuberculous mycobacteria (NTM) are ubiquitous bacteria that are naturally resistant to disinfectants and antibiotics and can colonize systems for supplying drinking water. Therefore, this study aimed to evaluate the prevalence of NTM in the drinking water of six hospitals in Tehran, Iran.
Methods
Totally, 198 water samples were collected. Each water sample was filtered via a membrane filter with a pore size of 0.45 µm and then decontaminated by 0.005% cetylpyridinium chloride. The membrane filters were incubated on two Lowenstein-Jensen media at 25 °C and 37 °C for 8 weeks. The positive cultures were identified with phenotypic tests, and then NTM species were detected according to the hsp65, rpoB, and 16S rDNA genes. Drug susceptibility testing (DST) was also carried out.
Results
Overall, 76 (40.4%) of the isolates were slowly growing mycobacteria (SGM) and 112 (59.6%) of the ones were rapidly growing mycobacteria (RGM). The most common NTM were Mycobacterium aurum, M. gordonae, M. phocaicum, M. mucogenicum, M. kansasii, M. simiae, M. gadium, M. lentiflavum, M. fortuitum, and M. porcinum. Among these 188 samples, NTM ranged from 1 to > 300 colony-forming unit (CFU) /500 mL, with a median of 182 CFU/500 mL. In the infectious department of all hospitals, the amount of CFU was higher than in other parts of the hospitals. The DST findings in this study indicated the diversity of resistance to different drugs. Among RGM, M. mucogenicum was the most susceptible isolate; however, M. fortuitum showed a different resistance pattern. Also, among SGM isolates, M. kansasii and M. simiae, the diversity of DST indicated.
Conclusions
The current study showed NTM strains could be an important component of hospital water supplies and a possible source of nosocomial infections according to the CFU reported in this study. The obtained findings also help clarify the dynamics of NTM variety and distribution in the water systems of hospitals in the research area.
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26
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Soezi M, Piri-Gavgani S, Ghanei M, Omrani MD, Soltanmohammadi B, Bagheri KP, Cohan RA, Vaziri F, Siadat SD, Fateh A, Khatami S, Azizi M, Rahimi-Jamnani F. Identification of a novel fully human anti-toxic shock syndrome toxin (TSST)-1 single-chain variable fragment antibody averting TSST-1-induced mitogenesis and cytokine secretion. BMC Biotechnol 2022; 22:31. [PMID: 36307814 PMCID: PMC9617332 DOI: 10.1186/s12896-022-00760-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 08/18/2022] [Accepted: 10/07/2022] [Indexed: 12/05/2022] Open
Abstract
Background Staphylococcal superantigens are virulence factors that help the pathogen escape the immune system and develop an infection. Toxic shock syndrome toxin (TSST)-1 is one of the most studied superantigens whose role in toxic shock syndrome and some particular disorders have been demonstrated. Inhibiting TSST-1 production with antibiotics and targeting TSST-1 with monoclonal antibodies might be one of the best strategies to prevent TSST-1-induced cytokines storm followed by lethality. Results A novel single-chain variable fragment (scFv), MS473, against TSST-1 was identified by selecting an scFv phage library on the TSST-1 protein. The MS473 scFv showed high affinity and specificity for TSST-1. Moreover, MS473 could significantly prevent TSST-1-induced mitogenicity (the IC50 value: 1.5 µM) and cytokine production. Conclusion Using traditional antibiotics with an anti-TSST-1 scFv as a safe and effective agent leads to deleting the infection source and preventing the detrimental effects of the toxin disseminated into the whole body. Supplementary information The online version contains supplementary material available at 10.1186/s12896-022-00760-8.
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Tavakoli R, Rahimi P, Hamidi-Fard M, Eaybpoush S, Doroud D, Ahmadi I, Anvari E, Aghasadeghi M, Fateh A. Comparing the expression levels of tripartite motif containing 28 in mild and severe COVID-19 infection. Virol J 2022; 19:156. [PMID: 36192760 PMCID: PMC9527726 DOI: 10.1186/s12985-022-01885-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Background Tripartite motif-containing 28 (TRIM28) is an impressive regulator of the epigenetic control of the antiviral immune response. This study evaluated if the differential expression of TRIM28 correlates with the severity of coronavirus disease 2019 (COVID-19) infection. Methods A total of 330 COVID-19 patients, including 188 mild and 142 severe infections, and 160 healthy controls were enrolled in this study. Quantitative real-time polymerase chain reaction (qPCR) was used to determine the expression levels of TRIM28 in the studied patients. Results TRIM28 mRNA levels were significantly lower in both groups of patients versus the control group and in the severe group indicated further reduction in comparison to mild infection. The multivariate logistic regression analysis showed the mean age, lower levels of low-density lipoprotein (LDL), high-density lipoprotein (HDL), cholesterol, lower 25-hydroxyvitamin D, and PCR cycle threshold (Ct) value and higher levels of erythrocyte sedimentation rate (ESR) and differential expression of TRIM28 were linked to the severity of COVID-19 infection. Conclusion The results of this study proved that the downregulation of TRIM28 might be associated with the severity of COVID-19 infection. Further studies are required to determine the association between the COVID-19 infection severity and TRIM family proteins.
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Affiliation(s)
- Rezvan Tavakoli
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Pooneh Rahimi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran.,Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Hamidi-Fard
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran.,Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eaybpoush
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- Quality Control Department, Production and Research Complex, Pasteur institute of Iran, Tehran, Iran
| | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Mohammadreza Aghasadeghi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran. .,Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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28
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Piri-Gavgani S, Ghanei M, Fateh A, Siadat SD, Nematollahi L, Rahimi-Jamnani F. Identification of two neutralizing human single-chain variable fragment antibodies targeting Staphylococcus aureus alpha-hemolysin. Iran J Basic Med Sci 2022; 25:1207-1214. [PMID: 36311199 PMCID: PMC9588317 DOI: 10.22038/ijbms.2022.64103.14253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/06/2022] [Indexed: 01/24/2023]
Abstract
OBJECTIVES The inability of the host immune system to defeat Staphylococcus aureus is due to various secreted virulent factors such as leukocidins, superantigens, and hemolysins, which interrupt the function of immune components. Alpha-hemolysin is one of the most studied cytolysins due to its pronounced effect on developing staphylococcal infections. Alpha-hemolysin-neutralizing antibodies are among the best candidates for blocking the toxin activity and preventing S. aureus pathogenesis. MATERIALS AND METHODS A human single-chain variable fragment (scFv) phage display library was biopanned against alpha-hemolysin. The selected phage clones were assessed based on their binding ability to alpha-hemolysin. The binding specificity and affinity of two scFvs (designated SP192 and SP220) to alpha-hemolysin were determined by enzyme-linked immunosorbent assay. Furthermore, the neutralizing activity of SP192 and SP220 was examined by concurrent incubation of rabbit red blood cells (RBCs) with alpha-hemolysin and scFvs. RESULTS SP192 and SP220 showed significant binding to alpha-hemolysin compared with the control proteins, including bovine serum albumin, human adiponectin, and toxic shock syndrome toxin-1. Besides, both scFvs showed high-affinity binding to alpha-hemolysin in the nanomolar range (Kaff: 0.9 and 0.7 nM-1, respectively), leading to marked inhibition of alpha-hemolysin-mediated lysis of rabbit RBCs (73% and 84% inhibition; respectively). CONCLUSION SP192 and SP220 scFvs can potentially be used as alpha-hemolysin-neutralizing agents in conjunction with conventional antibiotics to combat S. aureus infections.
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Affiliation(s)
- Somayeh Piri-Gavgani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Nematollahi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Leila Nematollahi. Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran. ; Fatemeh Rahimi Jamnani. Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran. ;
| | - Fatemeh Rahimi-Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran ,Corresponding authors: Leila Nematollahi. Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran. ; Fatemeh Rahimi Jamnani. Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran. ;
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Karimi AA, Tarharoudi R, Kianmehr Z, Sakhaee F, Jamnani FR, Siadat SD, Fateh A. Traces of JC polyomavirus in papillary thyroid cancer: a comprehensive study in Iran. Virol J 2022; 19:153. [PMID: 36163265 PMCID: PMC9513940 DOI: 10.1186/s12985-022-01881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background JC polyomavirus (JCPyV) is known to induce solid tumors such as astrocytomas, glioblastomas, and neuroblastomas in experimental animals, and recent studies have shown that the virus may be correlated with carcinogenesis. This study aimed to evaluate the impact of JCPyV on the progression of papillary thyroid cancer (PTC). Methods A total of 1057 samples, including 645 paraffin-embedded PTC biopsy samples (PEBS) and 412 fresh biopsy samples (FBS), and 1057 adjacent non-cancerous samples were evaluated for the presence of JCPyV DNA and RNA. Results We observed that 10.8% (114/1057) samples, including 17.5% (72/412) FBS and 6.5% (42/645) PEBS were positive for the JCPyV DNA. Among the JCPyV-positive samples, the mean JCPyV copy number was lower in patients with PEBS (0.3 × 10–4 ± 0.1 × 10–4 copies/cell) compared to FBS (1.8 × 10–1 ± 0.4 × 10–1 copies/cell) and non-PTC normal samples (0.2 × 10–5 ± 0.01 × 10–5 copies/cell), with a statistically significant difference (P < 0.001). The LT-Ag RNA expression was lower in PEBS than in FBS, while no VP1 gene transcript expression was found. Conclusions Although our results confirmed the presence of JCPyV in some Iranian patients with PTC, more research is needed to verify these results.
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Affiliation(s)
- Amir Ali Karimi
- Department of Biotechnology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Rahil Tarharoudi
- Department of Molecular and Cellular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Kianmehr
- Department of Biochemistry, Faculty of Biological Science, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, Nakhaeizadeh M, Kargarpour Kamakoli MA, Ebrahimifard N, Fateh A, Siadat SD, Vaziri F. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol 2022; 13:978355. [PMID: 36160200 PMCID: PMC9493315 DOI: 10.3389/fmicb.2022.978355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The 24-loci mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping has been used as an international standard method for Mycobacterium tuberculosis (Mtb) genotyping. However, different optimized VNTR loci sets for improving the discrimination of specific Mtb genotypes have been proposed. In this regard, we investigated the efficacy of accumulation of the percentage differences (APDs) compared with the least absolute shrinkage and selection operator (LASSO) regression strategy to identify a customized genotype-specific VNTR loci set which provides a resolution comparable to 24-loci MIRU-VNTR in divergent Mtb populations. We utilized Spoligotyping and 24-loci MIRU-VNTR typing for genotyping 306 Mtb isolates. The APD and LASSO regression approaches were used to identify a customized VNTR set in our studied isolates. Besides, the Hunter-Gaston discriminatory index (HGDI), sensitivity, and specificity of each selected loci set were calculated based on both strategies. The selected loci based on LASSO regression compared with APD-based loci showed a better discriminatory power for identifying all studied genotypes except for T genotype, which APD-based loci showed promising discriminative power. Our findings suggested the LASSO regression rather than the APD approach is more effective in the determination of possible discriminative VNTR loci set to precise discrimination of our studied Mtb population and may be beneficial to be used in finding reduced number loci sets in other Mtb genotypes or sublineages. Moreover, we proposed customized genotype-specific MIRU-VNTR loci sets based on the LASSO regression and APD approaches for precise Mtb strains identification. As the proposed VNTR sets offered a comparable discriminatory power to the standard 24 MIRU-VNTR loci set could be promising alternatives to the standard genotyping for using in resource-limited settings.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehran Nakhaeizadeh
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Nasim Ebrahimifard
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
- *Correspondence: Farzam Vaziri, ,
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31
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Basardeh E, Piri-Gavgani S, Soltanmohammadi B, Ghanei M, Omrani MD, Soezi M, Shokrgozar MA, Azizi M, Fateh A, Vaziri F, Siadat SD, Sharifzadeh Z, Rahimi-Jamnani F. Anti- Acinetobacter baumannii single-chain variable fragments show direct bactericidal activity. Iran J Basic Med Sci 2022; 25:1141-1149. [PMID: 36246061 PMCID: PMC9526879 DOI: 10.22038/ijbms.2022.64062.14106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/21/2022] [Indexed: 11/06/2022]
Abstract
Objectives The high resistance rate of Acinetobacter baumannii and the limited number of available antibiotics have prompted a worldwide effort to develop effective antimicrobial agents. Accordingly, identifying single-chain variable fragment antibodies (scFvs), capable of exerting direct antibacterial activity in an immune system-independent manner, may be making immunocompromised patients more susceptible to A. baumannii infections. Materials and Methods To isolate bactericidal scFvs targeting A. baumannii, we panned a large human scFv phage display library against whole-cell extensively drug-resistant (XDR) A. baumannii strains grown as biofilm or cultured with human blood or human peripheral blood mononuclear cells plus plasma. The binding of scFv-phages to A. baumannii was assessed by the dot-blot assay. Soluble scFvs, derived from the selected phages, were assessed based on their ability to bind and inhibit the growth of A. baumannii. Results Five phage clones showed the highest reactivity toward A. baumannii. Among five soluble scFvs, derived from positive phage clones, two scFvs, EB211 and EB279, had high expression yields and displayed strong binding to A. baumannii compared with the controls. Moreover, XDR A. baumannii strains treated with positively-charged scFvs, including EB211, EB279, or a cocktail of EB211 and EB279 (200 µg/ml), displayed lower viability (approximately 50%, 78%, and 40% viability, respectively) compared with PBS-treated bacteria. Conclusion These results suggest that combining last-resort antibiotics with bactericidal scFvs could provide promising outcomes in immunocompromised individuals with A. baumannii infections.
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Affiliation(s)
- Eilnaz Basardeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Somayeh Piri-Gavgani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnoush Soltanmohammadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdieh Soezi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Masoumeh Azizi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rahimi-Jamnani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran ,Corresponding author: Fatemeh Rahimi-Jamnani. Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran. Tel: +98-21-66953311; Fax: +98-21-66465132;
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32
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Ahmadi I, Afifipour A, Sakhaee F, Zamani MS, Mirzaei Gheinari F, Anvari E, Fateh A. Impact of interferon-induced transmembrane protein 3 gene rs12252 polymorphism on COVID-19 mortality. Cytokine 2022; 157:155957. [PMID: 35792282 PMCID: PMC9250290 DOI: 10.1016/j.cyto.2022.155957] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 01/08/2023]
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33
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Hadizadeh Tasbiti A, Badmasti F, Siadat SD, Fateh A, Yari F, GHzanfari Jajin M, Yari S. Recognition of specific immunogenic antigens with potential diagnostic value in multi-drug resistant Mycobacterium tuberculosis inducing humoral immunity in MDR-TB patients. Infect Genet Evol 2022; 103:105328. [PMID: 35788051 DOI: 10.1016/j.meegid.2022.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Tuberculosis (TB) as a public health crisis is caused by the intracellular bacterium Mycobacterium tuberculosis. Detection of immunogenic proteins in TB is valuable for the development of diagnostic tests, vaccine formulations and monitoring treatment outcome. In this study, we differentiated the immune-reactivity of proteins in multidrug-resistant tuberculosis (MDRTB) and drug-susceptible strains using purified anti-MDRTB antibodies isolated from inpatients. Our data showed that the anti- MDRTB antibody was well able to detect the MDR strain in the patient's sputum. The immunogenic proteins of MDRTB were purified by affinity chromatography and subjected to matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Analysis of the data revealed that seven MDRTB immunogenic proteins, including Rv2986c (HupB), Rv3699, Rv1133c (MetE), Rv0440 (GroEL), Rv3057c, Rv2558 and Rv2971 are involved in DNA stability, metabolism, cellular processes and some unknown functions. Similarities in the electrophoresis protein profiles were evident between the extracts of MDR and sensitive TB strains. However, the protein expression patterns of MDRTB isolates were distinguishable from that formed by susceptible TB strains.
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Affiliation(s)
- Alireza Hadizadeh Tasbiti
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran; Bacteriology Dept, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Yari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion, Iran
| | | | - Shamsi Yari
- Tuberculosis and Pulmonary Research Dept, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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34
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Khalilzadeh F, Sakhaee F, Sotoodehnejadnematalahi F, Zamani MS, Ahmadi I, Anvari E, Fateh A. Angiotensin-converting enzyme 2 rs2285666 polymorphism and clinical parameters as the determinants of COVID-19 severity in Iranian population. Int J Immunogenet 2022; 49:325-332. [PMID: 36029284 PMCID: PMC9539076 DOI: 10.1111/iji.12598] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]
Abstract
Host genetic factors may be correlated with the severity of coronavirus disease 2019 (COVID-19). Angiotensin-converting enzyme 2 (ACE2) plays a vital role in viral cell entrance. The current study aimed to evaluate the association of ACE2 rs2285666 polymorphism and clinical parameters with COVID-19 mortality. The ACE2 rs2285666 polymorphism was genotyped using the polymerase chain reaction-restriction fragment length polymorphism in 556 recovered and 522 dead patients. In this study, the frequency of ACE2 rs2285666 CC was significantly higher than TT genotype in dead patients. The multivariate logistic regression analysis results showed that the higher levels of alanine aminotransferase, alkaline phosphatase, creatinine, erythrocyte sedimentation rate, and C-reactive protein and the low levels of uric acid, cholesterol, low density lipoprotein, 25-hydroxyvitamin D, real-time PCR Ct values, and ACE2 rs2285666 CC genotype were associated with increased mortality rates after COVID-19. In conclusion, our findings demonstrated a possible link between COVID-19 mortality, clinical parameters, and ACE2 rs2285666 CC. Further research is required to confirm these results.
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Affiliation(s)
- Fereshteh Khalilzadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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35
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Raheem Juhi Al-Kaabi N, Khameneh SC, Montazeri M, Mardasi M, Amroabadi JM, Sakhaee F, Fateh A. On the relationship between tripartite motif-containing 22 single-nucleotide polymorphisms and COVID-19 infection severity. Hum Genomics 2022; 16:33. [PMID: 36028902 PMCID: PMC9412778 DOI: 10.1186/s40246-022-00394-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background The tripartite motif containing (TRIM)-22 participates in innate immune responses and exhibits antiviral activities. The present study aimed to assess of the relationship between TRIM22 single-nucleotide polymorphisms and clinical parameters with the coronavirus disease 2019 (COVID-19) infection severity.
Methods TRIM22 polymorphisms (rs7113258, rs7935564, and rs1063303) were genotyped using TaqMan polymerase chain reaction (PCR) assay in 495 dead and 497 improved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive patients.
Results In this study, the frequencies of TRIM22 rs1063303 GG, rs7935564 GG, and rs7113258 TT were significantly higher in dead patients than in improved patients, and higher viral load with low PCR Ct value was noticed in dead patients. The multivariate logistic regression analysis revealed that the lower levels of low-density lipoprotein (LDL), cholesterol, PCR Ct value, and lower 25-hydroxyvitamin D, and also higher levels of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and TRIM22 rs1063303 GG, rs7113258 TT, and rs3824949 GG genotypes were related to the COVID-19 infection severity.
Conclusion Our finding proved the probable relationship between the COVID-19 infection severity with the genotypes of TRIM22 SNPs and clinical parameters. More research is required worldwide to show the association between the COVID-19 infection severity and host genetic factors.
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Affiliation(s)
| | | | - Mohadeseh Montazeri
- Tissue Engineering and Biomaterials Research Center, National Institute of Genetic, Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahsa Mardasi
- Department of Plant Science and Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University G.C, Evin, Tehran, Iran
| | | | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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36
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Ghaderi F, Sotoodehnejadnematalahi F, Hajebrahimi Z, Fateh A, Siadat SD. Author Correction: Effects of active, inactive, and derivatives of Akkermansia muciniphila on the expression of the endocannabinoid system and PPARs genes. Sci Rep 2022; 12:12301. [PMID: 35854063 PMCID: PMC9296455 DOI: 10.1038/s41598-022-16591-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Farinaz Ghaderi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Zahra Hajebrahimi
- A&S Research Institute, Ministry of Science Research and Technology, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research and Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research and Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Sakhaee F, Mafi S, Zargar M, Vaziri F, Hajiesmaeili M, Siadat SD, Fateh A. Correlation between Legionella pneumophila serogroups isolated from patients with ventilator-associated pneumonia and water resources: a study of four hospitals in Tehran, Iran. Environ Sci Pollut Res Int 2022; 29:41368-41374. [PMID: 35089517 PMCID: PMC8796176 DOI: 10.1007/s11356-022-18867-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/21/2022] [Indexed: 05/08/2023]
Abstract
Legionella pneumophila (L. pneumophila) is one of the main pathogens, causing pneumonia and respiratory tract infections, especially in patients with ventilator-associated pneumonia (VAP). This study aimed to approve the hypothesis that the serogroup distribution of L. pneumophila isolates from patients is correlated with Legionella strains in the environment. A total of 280 bronchoalveolar lavage (BAL) samples from VAP patients admitted to the intensive care unit (ICU) as well as 116 water samples from different sources in four hospitals in Tehran, Iran, were evaluated for the presence of L. pneumophila infection by culture, nested polymerase chain reaction (PCR), real-time PCR, and sequencing for genetic diversity. The molecular and culture methods found 24 (8.6%) and 5 (1.8%) samples to be positive for L. pneumophila in VAP patients, while they found 23 (19.8%) and 8 (6.9%) positive samples in water resources, respectively. The sequencing results indicated that all positive clinical samples and 14 (60.8%) environmental samples were belonged to L. pneumophila serogroup 1. Smoking, age, length of ICU stay, and duration of ventilator use had strong relationship with L. pneumophila infectivity. In conclusion, this is the first report from Iran to determine minor differences in the serogroup distribution of environmental and clinical strains. However, further studies are needed to confirm this relationship in different regions of Iran.
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Affiliation(s)
- Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Shirin Mafi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohsen Zargar
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammadreza Hajiesmaeili
- Critical Care Quality Improvement Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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38
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Sakhaee F, Mosayebi Amroabadi J, Razi S, Vaziri F, Abdolrahimi F, Moghaddam S, Rahimi Jamnani F, Siadat SD, Fateh A. Detection of Mimivirus from respiratory samples in tuberculosis-suspected patients. Sci Rep 2022; 12:8676. [PMID: 35606506 PMCID: PMC9126102 DOI: 10.1038/s41598-022-12757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Acanthamoeba polyphaga mimivirus (APMV), a species of amoeba-infecting giant viruses, has recently emerged as human respiratory pathogens. This study aimed to evaluate the presence of Mimivirus in respiratory samples, collected from tuberculosis (TB)-suspected patients. The study was performed on 10,166 clinical respiratory samples from April 2013 to December 2017. Mimivirus was detected using a suicide nested-polymerase chain reaction (PCR) and real-time PCR methods. Of 10,166 TB-suspected patients, 4 (0.04%) were positive for Mimivirus, including Mimivirus-53, Mimivirus-186, Mimivirus-1291, and Mimivirus-1922. Three out of four patients, hospitalized in the intensive care unit (ICU), were mechanically ventilated. All patients had an underlying disease, and the virus was detected in both sputum and bronchoalveolar lavage samples. In conclusion, Mimivirus was isolated from TB-suspected patients in a comprehensive study. The present results, similar to previous reports, showed that Mimiviruses could be related to pneumonia. Further studies in different parts of the world are needed to additional investigate the clinical importance of Mimivirus infection.
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Tarashi S, Zamani MS, Bahramali G, Fuso A, Vaziri F, Karimipoor M, Fateh A, Siadat SD. RNA Expression Analysis of Mycobacterial Methyltransferases Genes in Different Resistant Strains of Mycobacterium tuberculosis. Iran Biomed J 2022; 26:240-251. [PMID: 35216515 PMCID: PMC9440689 DOI: 10.52547/ibj.26.3.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/03/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Tuberculosis infection still represents a global health issue affecting patients worldwide. Strategies for its control may be not as effective as it should be, specifically in case of resistant strains of Mycobacterium tuberculosis (M.tb.) In this regard, the role of mycobacterial methyltransferases (MTases) in TB infection can be fundamental, though it has not been broadly deciphered. METHODS Five resistant isolates of M.tb were obtained. M.tb H37Rv (ATCC 27249) was used as a reference strain. Seven putative mycobacterial MTase genes (Rv0645c, Rv2966c, Rv1988, Rv1694, Rv3919c, Rv2756c, and Rv3263) and Rv1392 as SAM synthase were selected for analysis. PCR-sequencing and qRT-PCR were performed to compare mutations and expression levels of MTases in different strains. The 2-ΔΔCt method was employed to calculate the relative expression levels of these genes. RESULTS Only two mutations were found in isoniazid resistance (INHR) strain for Rv3919c (T to G in codon 341) and Rv1392 (G to A in codon 97) genes. Overexpression of Rv0645c, Rv2756c, Rv3263, and Rv2966c was detected in all sensitive and resistant isolates. However, Rv1988 and Rv3919c decreased and Rv1694 increased in the sensitive strains. The Rv1392 expression level also decreased in INHR isolate. CONCLUSION We found a correlation between mycobacterial MTases expression and resistance to antibiotics in M.tb strains. Some MTases undeniably are virulence factors that specifically hijack the host defense mechanism. Further evaluations are needed to explore the complete impact of mycobacterial MTases within specific strains of M.tb to introduce novel diagnosis and treatment strategies.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Golnaz Bahramali
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, Italy
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Ostadmohammadi S, Nojoumi SA, Fateh A, Siadat SD, Sotoodehnejadnematalahi F. Interaction between Clostridium species and microbiota to progress immune regulation. Acta Microbiol Immunol Hung 2022:2022.01678. [PMID: 35397157 DOI: 10.1556/030.2022.01678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/18/2022] [Indexed: 11/19/2022]
Abstract
Gut microbiota can interact with the immune system through direct or indirect pathways. In the indirect pathway, gut microbiota produces metabolites such as short chain fatty acids (SCFAs), which may modulate the immune response. SCFAs reduce inflammation, repair intestinal barrier, and induce propagation of specific immune cells, e.g., T regulatory cells (Treg), which can suppress reactive cells such as macrophage and dendritic cells (DCs). As one of the most dominant members of microbiota, Clostridium produces SCFAs. As one of SCFA members, butyrate plays an important role in the modulation of immune cells. Through butyrate production, Clostridium helps to generate aryl hydrocarbon receptor (AhR). AhR interacts with many proteins inside the cytoplasm including Heat Shock Protein 90 (HSP 90), HSP 23, and chaperone. Activation of AhR leads to its translocation inside the nucleus and gene expression, which yields cell differentiation, energy metabolism, microbial defense, and immune cell propagation. Moreover, it may interact with other cells like B-cell and epithelial cell, which are responsible for modulation and maturation, respectively. AhR causes upregulation in the co-stimulatory marker in the DCs and interacts with nuclear factor KB (NF-ĸB) to modulate cell function. Butyrate induces Treg (iTreg) propagation and upregulates the Forkhead box p3 (FOXP3) as a special marker of Treg cell. It may also yield signaling through G-protein coupled receptors (GPRs) which, in turn, facilitates polymorphonuclear (PMN) chemotaxis.The interaction between microbiota and non-immune cells, such as Paneth cells, leads to the secretion of antimicrobial substance, erection of barriers against bacterial pathogens, and regulation of microbiota composition via feedback effect. In addition, the components released from microbiota, such as peptidoglycan, reinforce the maturation of both the immune system and non-immune tissue development. Moreover, microbiota can directly activate the effector cells, e.g., macrophage, to secrete cytokines and propagate Treg cells.
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Affiliation(s)
- Soheila Ostadmohammadi
- 1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Ali Nojoumi
- 2Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- 3Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- 2Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- 3Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- 2Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- 3Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Mirlohi SH, Eftekhari K, Shirzadi R, Fateh A, Masoumi M, Modaresi M. The Value of Sputum Polymerase Chain Reaction for Detection of Nontuberculous Mycobacteria in Cystic Fibrosis Patients with Negative Nontuberculous Mycobacteria Sputum Culture. Med J Islam Repub Iran 2022; 36:7. [PMID: 35999933 PMCID: PMC9386751 DOI: 10.47176/mjiri.36.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
Background: Cystic Fibrosis (CF) is a life-threatening autosomal recessive disease. The purpose of this study was to evaluate the value of Polymerase Chain Reaction (PCR) in CF patients with Nontuberculous Mycobacteria (NTM) negative sputum culture.
Methods: This is a descriptive cross-sectional study. The population included all children with CF, aged between 5 - 18 years old, with an NTM negative sputum culture. The patient's sputum samples were sent for smear and culture of NTM, RFLP PCR, and PCR sequence.
Results: In total, 57 CF patients with negative NTM sputum culture were enrolled. Nine patients (15.78%) had positive sputum PCR for NTM. Among these strains, Mycobacterium simiae was the most common one with 5 cases (8.77% of total positive cases). Conclusion: PCR can be used as an alternative diagnostic method for NTM in CF patients with negative NTM sputum culture, always under clinical suspicion of the disease.
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Affiliation(s)
- Seyed Hossein Mirlohi
- Pediatric Respiratory and Sleep Medicine Research Center, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Kambiz Eftekhari
- Pediatric Gastroenterology and Hepatology Research Center, Department of Pediatrics, Bahrami Children’s Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Rohola Shirzadi
- Pediatric Respiratory and Sleep Medicine Research Center, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammadreza Modaresi
- Pediatric Respiratory and Sleep Medicine Research Center, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding author: Dr Mohammadreza Modaresi,
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Hassani S, Sotoodehnejadnematalahi F, Fateh A, Siadat SD. Evaluation of Association between Bifidobacterium bifidum Derived Extracellular Vesicles and Intestinal Epithelium Tight Junction Proteins through Notch-1 and AhR Activation in Caco-2 Cell Line. Mol Genet Microbiol Virol 2021; 36:S1-S6. [DOI: 10.3103/s0891416821050086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 10/13/2023]
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Rahimi P, Tarharoudi R, Rahimpour A, Mosayebi Amroabadi J, Ahmadi I, Anvari E, Siadat SD, Aghasadeghi M, Fateh A. The association between interferon lambda 3 and 4 gene single-nucleotide polymorphisms and the recovery of COVID-19 patients. Virol J 2021; 18:221. [PMID: 34775984 PMCID: PMC8590865 DOI: 10.1186/s12985-021-01692-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The recent pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has elevated several clinical and scientific questions. These include how host genetic factors influence the pathogenesis and disease susceptibility. Therefore, the aim of this study was to evaluate the impact of interferon lambda 3 and 4 (IFNL3/4) gene polymorphisms and clinical parameters on the resistance and susceptibility to coronavirus disease 2019 (COVID-19) infection. METHODS A total of 750 SARS-CoV-2 positive patients (375 survivors and 375 nonsurvivors) were included in this study. All single-nucleotide polymorphisms (SNPs) on IFNL3 (rs12979860, rs8099917, and rs12980275) and IFNL4 rs368234815 were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS In this study, a higher viral load (low PCR Ct value) was shown in nonsurvivor patients. In survivor patients, the frequency of the favorable genotypes of IFNL3/4 SNPs (rs12979860 CC, rs12980275 AA, rs8099917 TT, and rs368234815 TT/TT) was significantly higher than in nonsurvivor patients. Multivariate logistic regression analysis has shown that a higher low-density lipoprotein (LDL), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and PCR Ct value, and lower 25-hydroxyvitamin D, and also IFNL3 rs12979860 TT, IFNL3 rs8099917 GG, IFNL3 rs12980275 GG, and IFNL4 rs368234815 ∆G/∆G genotypes were associated with the severity of COVID-19 infection. CONCLUSIONS The results of this study proved that the severity of COVID-19 infection was associated with clinical parameters and unfavorable genotypes of IFNL3/IFNL4 SNPs. Further studies in different parts of the world are needed to show the relationship between severity of COVID-19 infection and host genetic factors.
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Affiliation(s)
- Pooneh Rahimi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Rahil Tarharoudi
- Department of Molecular and Cellular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Rahimpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammadreza Aghasadeghi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran.
- Viral Vaccine Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Soltanmohammadi B, Piri‐Gavgani S, Basardeh E, Ghanei M, Azizi M, Khaksar Z, Sharifzadeh Z, Badmasti F, Soezi M, Fateh A, Azimi P, Siadat SD, Shooraj F, Bouzari S, Omrani MD, Rahimi‐Jamnani F. Bactericidal fully human single-chain fragment variable antibodies protect mice against methicillin-resistant Staphylococcus aureus bacteraemia. Clin Transl Immunology 2021; 10:e1302. [PMID: 34221401 PMCID: PMC8240403 DOI: 10.1002/cti2.1302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/01/2021] [Accepted: 05/30/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The increasing prevalence of antibiotic-resistant Staphylococcus aureus, besides the inadequate numbers of effective antibiotics, emphasises the need to find new therapeutic agents against this lethal pathogen. METHODS In this study, to obtain antibody fragments against S. aureus, a human single-chain fragment variable (scFv) library was enriched against living methicillin-resistant S. aureus (MRSA) cells, grown in three different conditions, that is human peripheral blood mononuclear cells with plasma, whole blood and biofilm. The antibacterial activity of scFvs was evaluated by the growth inhibition assay in vitro. Furthermore, the therapeutic efficacy of anti-S. aureus scFvs was appraised in a mouse model of bacteraemia. RESULTS Three scFv antibodies, that is MEH63, MEH158 and MEH183, with unique sequences, were found, which exhibited significant binding to S. aureus and reduced the viability of S. aureus in in vitro inhibition assays. Based on the results, MEH63, MEH158 and MEH183, in addition to their combination, could prolong the survival rate, reduce the bacterial burden in the blood and prevent inflammation and tissue destruction in the kidneys and spleen of mice with MRSA bacteraemia compared with the vehicle group (treated with normal saline). CONCLUSION The combination therapy with anti-S. aureus scFvs and conventional antibiotics might shed light on the treatment of patients with S. aureus infections.
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Affiliation(s)
- Behnoush Soltanmohammadi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Somayeh Piri‐Gavgani
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Eilnaz Basardeh
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Mostafa Ghanei
- Chemical Injuries Research CenterSystems Biology and Poisoning InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Masoumeh Azizi
- Molecular Medicine Department, Biotechnology Research CenterPasteur Institute of IranTehranIran
| | - Zabihollah Khaksar
- Department of Basic SciencesSchool of Veterinary MedicineShiraz UniversityShirazIran
| | | | - Farzad Badmasti
- Department of BacteriologyPasteur Institute of IranTehranIran
| | - Mahdieh Soezi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Parisa Azimi
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Fahimeh Shooraj
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
| | - Saeid Bouzari
- Molecular Biology DepartmentPasteur Institute of IranTehranIran
| | - Mir Davood Omrani
- Department of Medical GeneticsSchool of MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Fatemeh Rahimi‐Jamnani
- Department of Mycobacteriology and Pulmonary ResearchPasteur Institute of IranTehranIran
- Microbiology Research CenterPasteur Institute of IranTehranIran
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Ghaemi F, Fateh A, Sepahy AA, Zangeneh M, Ghanei M, Siadat SD. Blood microbiota composition in Iranian pre-diabetic and type 2 diabetic patients. Hum Antibodies 2021; 29:243-248. [PMID: 34151785 DOI: 10.3233/hab-210450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Type 2 diabetes as the most prevalent metabolic disorder, is one of the major causes of morbidity and mortality worldwide. Recent studies suggest that body microbiota may play a role in developing metabolic disorders including type 2 diabetes. The objective of the present study was to investigate the blood microbiota composition in Iranian pre-diabetic and type 2 diabetic patients compared to healthy individuals. METHODS Blood samples were taken after 12-h fasting from 90 participants, 30 healthy individuals, 30 type 2 diabetes patients and 30 pre-diabetic participants. The buffy coat layer separated by centrifugation at 800 and DNA was extracted using a column-based method. Composition and load of blood microbiota was evaluated by real-time PCR method using genus specific 16S rRNA primers. RESULTS The load of Akkermansia, and Faecalibacterium was higher in normal volunteers compared to pre-diabetic and type 2 diabetes group (p< 0.05).The load of Bifidobacterium was higher in normal volunteers compared to type 2 diabetes patients (p= 0.02).In contrast, the load of Lactobacillus and Escherichia coli was higher in pre-diabetics and type 2 diabetes patients compared to normal volunteers (p< 0.05).The load of Bacteroides fragilis was not statistically different between studied groups but it was higher in males compared to female group (p= 0.04). the load of other bacteria was not significantly different between male and female participants. CONCLUSION There is difference between microbiota composition in white blood cells of pre-diabetic and type 2 diabetes patients compared to healthy people. Determination of blood microbiota pattern may have a role in diagnosis and preventive of type 2 diabetes in a certain population. For more clarification about correlation between blood microbiota and type 2 diabetes, larger studies with more participants in different ethnical populations is suggested.
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Affiliation(s)
- Farahnaz Ghaemi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abbas Akhavan Sepahy
- Department of Microbiology, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Mehrangiz Zangeneh
- Department of Infectious Diseases, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Yaghoubfar R, Behrouzi A, Zare Banadkoki E, Ashrafian F, Lari A, Vaziri F, Nojoumi SA, Fateh A, Khatami S, Siadat SD. Effect of Akkermansia muciniphila, Faecalibacterium prausnitzii, and Their Extracellular Vesicles on the Serotonin System in Intestinal Epithelial Cells. Probiotics Antimicrob Proteins 2021; 13:1546-1556. [PMID: 33852147 DOI: 10.1007/s12602-021-09786-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The gastrointestinal (GI) tract is an essential reservoir of serotonin or 5-hydroxytryptamine (5-HT), which possesses a set of bacterial species communities. Intestinal microbiota has the ability to modulate the host's serotonin system. In this regard, we evaluated the effect of Akkermansia muciniphila and Faecalibacterium prausnitzii along with their extracellular vesicles (EVs) on serotonin system-related genes in human epithelial colorectal adenocarcinoma (Caco-2) cells. The differentiated Caco-2 cells were treated with A. muciniphila and F. prausnitzii with the multiplicity of infection ratio of 1 and 10 and the EV concentration of 1 μg/mL and 50 μg/mL, respectively. After 24 h, the serotonin level was quantified using an ELISA kit and also the gene expression of serotonin system-related genes was examined using the quantitative real-time PCR method. According to the results, treatment with A. muciniphila and F. prausnitzii-derived EVs increased the serotonin level, while none of the bacteria could affect the serotonin level in the Caco-2 cells. Both bacteria had significant effects on the mRNA expression of serotonin system-related genes in the Caco-2 cells. Moreover, we observed that A. muciniphila and F. prausnitzii-derived EVs could impact the expression of major genes involved in the serotonin system. Our findings showed that A. muciniphila and F. prausnitzii along with their EVs could modulate serotonin system-related genes; hence, they may be useful in microbiota modulation therapies to maintain the homeostasis of the serotonin system.
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Affiliation(s)
- Rezvan Yaghoubfar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ava Behrouzi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Ashrafian
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Arezou Lari
- Systems Biomedicine Unit, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Hadifar S, Mostafaei S, Behrouzi A, Fateh A, Riahi P, Siadat SD, Vaziri F. Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line. BMC Bioinformatics 2021; 22:154. [PMID: 33765916 PMCID: PMC7992940 DOI: 10.1186/s12859-021-04100-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/23/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND A growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain-specific behavior of Mycobacterium tuberculosis (M.tb) population, the etiological agent of TB infection in this association has been neglected. In this context, this study was conducted to investigate this association with consideration of the genetic background of strains in the M.tb population. RESULTS We employed the elastic net penalized logistic regression model, as a statistical-learning algorithm for gene selection, to evaluate this association in 129 genes involved in TLRs and NF-κB signaling pathways in response to two different M.tb sub-lineage strains (L3-CAS1and L 4.5). Of the 129 genes, 21 were found to be associated with the two studied M.tb sub-lineages. In addition, MAPK8IP3 gene was identified as a novel gene, which has not been reported in previous lung cancer studies and may have the potential to be recognized as a novel biomarker in lung cancer investigation. CONCLUSIONS This preliminary study provides new insights into the mechanistic association between TB infection and lung cancer. Further mechanistic investigations of this association with a large number of M.tb strains, encompassing the other main M.tb lineages and using the whole transcriptome of the host cell are inevitable.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Epidemiology and Biostatistics Unit, Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ava Behrouzi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parisa Riahi
- Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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48
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Kargarpour Kamakoli M, Hadifar S, Khanipour S, Farmanfarmaei G, Fateh A, Mostafaei S, Siadat SD, Vaziri F. Tuberculosis under the Influence of COVID-19 Lockdowns: Lessons from Tehran, Iran. mSphere 2021; 6:e00076-21. [PMID: 33627506 PMCID: PMC8544884 DOI: 10.1128/msphere.00076-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
This study investigates the short-term effects of the coronavirus disease 2019 (COVID-19) pandemic lockdown on tracing and detection of tuberculosis (TB) patients in Tehran, Iran. Results of this study have demonstrated that due to the significant decrease in the identification of patients with suspected TB during the COVID-19 outbreak in Tehran, it is imperative that patients with suspected TB be tracked and diagnosed more quickly to make up for some of the decline in TB diagnosis in recent months and to recover lost cases.
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Affiliation(s)
- Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ghazaleh Farmanfarmaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah, Iran
- Epidemiology and Biostatistics Unit, Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Yaghoubfar R, Behrouzi A, Fateh A, Nojoumi SA, Vaziri F, Khatami S, Siadat SD. Effects of Akkermansia muciniphila and Faecalibacterium prausnitzii on serotonin transporter expression in intestinal epithelial cells. J Diabetes Metab Disord 2021; 20:1-5. [PMID: 34222056 DOI: 10.1007/s40200-020-00539-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
Purpose The highest level of peripheral serotonin in the body can be found in the gastrointestinal (GI) tract as its reservoir. There is complete interaction between human gastrointestinal microbiota and serotonin system. Serotonin in the GI is transferred by serotonin transporters (SERTs), which play a crucial role in the bioavailability of serotonin in the GI. SERT impairment is associated with the pathology of GI disorders. It is known that intestinal microbiota can regulate the SERT function. Therefore, it may be useful to regulate of SERT expression by modulation of microbiota and improvement of intestinal motility and GI sensation. In this study, we aimed to evaluate the effects of two next-generation probiotics, including Akkermansia muciniphila and Faecalibacterium prausnitzii, and their supernatants on SERT gene expression in human epithelial colorectal adenocarcinoma cells (Caco-2). Methods The Caco-2 cells were treated with multiplicity of infection (MOI) ratio of 100 of A. muciniphila and F. prausnitzii, as well as their supernatants. After 24 h, SERT gene expression was examined by quantitative real-time polymerase chain reaction (qRT-PCR) assay. Results A. muciniphila up-regulated the SERT mRNA level by 3.01 folds, compared to the control group. F. prausnitzii, similar to A. muciniphila, increased the expression of SERT gene in Caco-2 cells by 3.43 folds (P < 0.001). Moreover, the supernatants of A. muciniphila and F. prausnitzii significantly up-regulated the expression of SERT gene in the cell line by 2.4 and 5.7 folds, respectively, compared to the control group (P < 0.001). Conclusions The present results showed that A. muciniphila and F. prausnitzii, as well as their supernatants, increased the expression of SERT gene in Caco-2 cells. Therefore, they might be helpful in the microbiota-modulating treatment of inflammatory bowel diseases.
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Affiliation(s)
- Rezvan Yaghoubfar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ava Behrouzi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Hadifar S, Fateh A, Pourbarkhordar V, Siadat SD, Mostafaei S, Vaziri F. Variation in Mycobacterium tuberculosis population structure in Iran: a systemic review and meta-analysis. BMC Infect Dis 2021; 21:2. [PMID: 33397308 PMCID: PMC7784266 DOI: 10.1186/s12879-020-05639-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/19/2020] [Indexed: 01/30/2023] Open
Abstract
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.
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Affiliation(s)
- Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Pourbarkhordar
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Epidemiology and Biostatistics Unit, Rheumatology Research Centre, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Centre (MRC), Pasteur Institute of Iran, Tehran, Iran.
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