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Abed S, Sholeh M, Khazani Asforooshani M, Shafiei M, Hashemi Shahraki A, Nasr S. Insights into the novel Enterococcus faecalis phage: A comprehensive genome analysis. PLoS One 2024; 19:e0301292. [PMID: 38743671 PMCID: PMC11093359 DOI: 10.1371/journal.pone.0301292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 05/16/2024] Open
Abstract
Enterococcus faecalis, a Gram-positive bacterium, poses a significant clinical challenge owing to its intrinsic resistance to a broad spectrum of antibiotics, warranting urgent exploration of innovative therapeutic strategies. This study investigated the viability of phage therapy as an alternative intervention for antibiotic-resistant E. faecalis, with a specific emphasis on the comprehensive genomic analysis of bacteriophage SAM-E.f 12. The investigation involved whole-genome sequencing of SAM-E.f 12 using Illumina technology, resulting in a robust dataset for detailed genomic characterization. Bioinformatics analyses were employed to predict genes and assign functional annotations. The bacteriophage SAM-E.f 12, which belongs to the Siphoviridae family, exhibited substantial potential, with a burst size of 5.7 PFU/infected cells and a latent period of 20 min. Host range determination experiments demonstrated its effectiveness against clinical E. faecalis strains, positioning SAM-E.f 12 as a precise therapeutic agent. Stability assays underscore resilience across diverse environmental conditions. This study provides a comprehensive understanding of SAM-E.f 12 genomic composition, lytic lifecycle parameters, and practical applications, particularly its efficacy in murine wound models. These results emphasize the promising role of phage therapy, specifically its targeted approach against antibiotic-resistant E. faecalis strains. The nuanced insights derived from this research will contribute to the ongoing pursuit of efficacious phage therapies and offer valuable implications for addressing the clinical challenges associated with E. faecalis infections.
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Affiliation(s)
- Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, United States of America
| | - Shaghayegh Nasr
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Microorganisms Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
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Hashemi Shahraki A, Vahed M, Mirsaeidi M. Genome sequencing of Pseudomonas aeruginosa phages; UF_RH7 and UF_RH9. Microbiol Resour Announc 2024; 13:e0105023. [PMID: 38483455 PMCID: PMC11008205 DOI: 10.1128/mra.01050-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/03/2024] [Indexed: 04/12/2024] Open
Abstract
We have sequenced the genomes of two lytic phages, UF_RH7 and UF_RH9, which infect Pseudomonas aeruginosa. UF_RH7 belongs to Casjensviridae family and has a genome length of 58,217 bp and encodes 82 proteins. UF_RH9 belongs to Caudoviricetes class and has a genome length of 42,609 bp and encodes 55 proteins.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
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Vaeli Zadeh A, Dinparastisaleh R, Vaezi A, Bandyopadhyay D, Rubinstein I, Baig HZ, Calderon-Candelario R, Hashemi Shahraki A, Kawasaki T, Magnusson JM, Larsson LO, Sharafkhaneh A, Herazo-Maya JD, Lee AS, Mirsaeidi M. Risk of 30-Day All-Cause Readmission in Interstitial Lung Disease Patients after COVID-19: National-Level Data. Ann Am Thorac Soc 2024; 21:428-437. [PMID: 38134434 PMCID: PMC10913765 DOI: 10.1513/annalsats.202305-491oc] [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: 05/30/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023] Open
Abstract
Rationale: Hospital readmission within 30 days poses challenges for healthcare providers, policymakers, and patients because of its impact on care quality, costs, and outcomes. Patients with interstitial lung disease (ILD) are particularly affected by readmission, which is associated with increased morbidity and mortality and reduced quality of life. Because small sample sizes have hindered previous studies, this study seeks to address this gap in knowledge by examining a large-scale dataset. Objective: To determine the rate and probability of 30-day all-cause readmission and secondary outcomes in patients with coronavirus disease (COVID-19) or ILD admitted to the hospital. Methods: This study is a nested cohort study that used the PearlDiver patient records database. Adult patients (age ⩾18 yr) who were admitted to hospitals in 28 states in the United States with COVID-19 or ILD diagnoses were included. We defined and analyzed two separate cohorts in this study. The first cohort consisted of patients with COVID-19 and was later divided into two groups with or without a history of ILD. The second cohort consisted of patients with ILD and was later divided into groups with COVID-19 or with a non-COVID-19 pneumonia diagnosis at admission. We also studied two other subcohorts of patients with and without idiopathic pulmonary fibrosis within the second cohort. Propensity score matching was employed to match confounders between groups. The Kaplan-Meier log rank test was applied to compare the probabilities of outcomes. Results: We assessed the data of 2,286,775 patients with COVID-19 and 118,892 patients with ILD. We found that patients with COVID-19 with preexisting ILD had an odds ratio of 1.6 for 30-day all-cause readmission. Similarly, an odds ratio of 2.42 in readmission rates was observed among hospitalized individuals with ILD who contracted COVID-19 compared with those who were hospitalized for non-COVID-19 pneumonia. Our study also found a significantly higher probability of intensive care admission among patients in both cohorts. Conclusions: Patients with ILD face heightened rates of hospital readmissions, particularly when ILD is combined with COVID-19, resulting in adverse outcomes such as decreased quality of life and increased healthcare expenses. It is imperative to prioritize preventive measures against COVID-19 and establish effective postdischarge care strategies for patients with ILD.
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Affiliation(s)
- Ali Vaeli Zadeh
- University of Miami at Holy Cross Health, Fort Lauderdale, Florida
| | - Roshan Dinparastisaleh
- Division of Pulmonary, Critical Care, and Sleep, College of Medicine – Jacksonville, University of Florida, Jacksonville, Florida
| | - Atefeh Vaezi
- Division of Pulmonary, Critical Care, and Sleep, College of Medicine – Jacksonville, University of Florida, Jacksonville, Florida
| | | | - Israel Rubinstein
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Illinois
| | - Hassan Z. Baig
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida
| | | | - Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care, and Sleep, College of Medicine – Jacksonville, University of Florida, Jacksonville, Florida
| | | | - Jesper M. Magnusson
- Department of Pulmonology, Institute of Medicine, Shagreens Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars-Olof Larsson
- Division of Respiratory Medicine, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden; and
| | - Amir Sharafkhaneh
- Department of Medicine, Pulmonary, Critical Medicine and Sleep Medicine, Baylor College of Medicine, Houston, Texas
| | - Jose D. Herazo-Maya
- Department of Internal Medicine, University of South Florida, Tampa, Florida
| | - Augustine S. Lee
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, and Sleep, College of Medicine – Jacksonville, University of Florida, Jacksonville, Florida
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Ghodousi A, Darban-Sarokhalil D, Shahraki AH, Shanmugam S. Editorial: Genomics-based strategies for advanced drug resistance and epidemiological surveillance of Mycobacterium tuberculosis and other non-tuberculous mycobacteria. Front Microbiol 2023; 14:1264285. [PMID: 37680533 PMCID: PMC10482242 DOI: 10.3389/fmicb.2023.1264285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 09/09/2023] Open
Affiliation(s)
- Arash Ghodousi
- Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University, Milan, Italy
| | - Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Sadeghi J, Hashemi Shahraki A, Chaganti SR, Heath D. Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health. Environ Res 2023; 231:116298. [PMID: 37268212 DOI: 10.1016/j.envres.2023.116298] [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: 12/06/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023]
Abstract
Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | | | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Hashemi Shahraki A, Vahed M, Dinparastisaleh R, Mirsaeidi M. Complete Genome Sequencing of a Novel Pseudomonas aeruginosa Phage, UF_RH5. Microbiol Resour Announc 2023:e0039623. [PMID: 37338387 DOI: 10.1128/mra.00396-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Here, we introduce UF_RH5, a novel lytic phage targeting clinically isolated Pseudomonas aeruginosa. It belongs to the Siphovirus morphology family, Septimatrevirus genus, with a 42,566-bp genome with a GC content of 53.60%, encoding 58 proteins. Under electron microscopy, UF_RH5 exhibits a length of 121 nm and a capsid size of 45 nm.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Roshan Dinparastisaleh
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, USA
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Hashemi Shahraki A, Vahed M, Masood S, Mirsaeidi M. Complete Genome Sequence of Pseudomonas aeruginosa Phage UF_RH6, Isolated from Human Lung. Microbiol Resour Announc 2023:e0020623. [PMID: 37249420 DOI: 10.1128/mra.00206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
We report the genome sequence of a lytic phage named UF_RH6, which infects Pseudomonas aeruginosa. This phage was isolated from a respiratory secretion sample from a patient with pulmonary P. aeruginosa. UF_RH6 belongs to the family Caudoviricetes and the genus Samunavirus. Its genome is 94,715 bp in length and encodes 130 proteins.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Shahla Masood
- Department of Pathology and Laboratory Medicine, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
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Hashemi Shahraki A, Vahed M, Mirsaeidi M. Complete Genome Sequencing of the Novel Pseudomonas aeruginosa Phage UF_RH1. Microbiol Resour Announc 2023:e0013923. [PMID: 37166313 DOI: 10.1128/mra.00139-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Here, we present the genome sequence of a novel Pseudomonas aeruginosa bacteriophage called UF_RH1. This lytic phage has a genome size of 42,567 bp and is classified as a member of the Siphoviridae family and the Septimatrevirus genus. UF_RH1 shares genetic similarities with Stenotrophomonas phage vB_SmaS-DLP_2.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Majid Vahed
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, Florida, USA
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Chaganti SR, Plouff C, Madani M, Shahraki AH, Vasquez AA, Seth R, Heath DD, Ram JL. Variation in the diversity of bacterial communities and potential sources of fecal contamination of beaches in the Huron to Erie corridor. Water Res 2022; 222:118913. [PMID: 35940154 DOI: 10.1016/j.watres.2022.118913] [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: 02/28/2022] [Revised: 07/03/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.
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Affiliation(s)
- Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Claire Plouff
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States
| | - Mohammad Madani
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | | | - Adrian A Vasquez
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States
| | - Rajesh Seth
- Department of Civil & Environmental Engineering, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
| | - Jeffrey L Ram
- Belle Isle Aquarium Field Research Laboratory, Facility of Healthy Urban Waters, Department of Physiology, Wayne State University, Detroit, MI 48201, United States; Department of Physiology, Wayne State University, 540 E. Canfield St., Detroit, MI 48201, United States.
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Shahraki AH, Tian R, Zhang C, Fregien NL, Bejarano P, Mirsaeidi M. Anti-inflammatory Properties of the Alpha-Melanocyte-Stimulating Hormone in Models of Granulomatous Inflammation. Lung 2022; 200:463-472. [PMID: 35717488 PMCID: PMC9360058 DOI: 10.1007/s00408-022-00546-x] [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: 04/17/2022] [Accepted: 05/29/2022] [Indexed: 11/08/2022]
Abstract
Purpose Alpha-melanocyte stimulating hormone (α-MSH) is known to have anti-inflammatory effects. However, the anti-inflammatory properties of α-MSH on normal bronchial epithelial cells are largely unknown, especially in the context of in vitro sarcoidosis models. Methods We evaluated the anti-inflammatory effects of α-MSH on two different in vitro sarcoidosis models (lung-on-membrane model; LOMM and three-dimensional biochip pulmonary sarcoidosis model; 3D-BSGM) generated from NBECs and an in vivo sarcoidosis mouse model. Results Treatment with α-MSH decreased inflammatory cytokine levels and downregulated type I interferon pathway genes and related proteins in LOMM and 3D-BSGM models. Treatment with α-MSH also significantly decreased macrophages and cytotoxic T-cells counts in a sarcoidosis mice model. Conclusion Our results confirm the direct role of type I IFNs in the pathogenesis of sarcoid lung granulomas and highlight α-MSH as a potential novel therapeutic agent for treating pulmonary sarcoidosis. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00408-022-00546-x.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, 655 West 11th Street, Jacksonville, FL, 32209, USA
| | - Runxia Tian
- Department of Cell Biology, University of Miami, Miami, FL, USA
| | - Chongxu Zhang
- Department of Cell Biology, University of Miami, Miami, FL, USA
| | - Nevis L Fregien
- Department of Cell Biology, University of Miami, Miami, FL, USA
| | - Pablo Bejarano
- Department of Pathology, Cleveland Clinic, Weston, FL, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, 655 West 11th Street, Jacksonville, FL, 32209, USA.
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Sadeqi S, Hashemi Shahraki A, Nikkhahi F, Javadi A, Amin Marashi SM. Application of bacteriophage cocktails for reducing the bacterial load of nosocomial pathogens in hospital wastewater. Iran J Microbiol 2022; 14:395-401. [PMID: 37124863 PMCID: PMC10132342 DOI: 10.18502/ijm.v14i3.9782] [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: 05/02/2023]
Abstract
Background and Objectives In the third world and developing countries, hospital sewage is mixed with municipal wastewater. The treated effluent contains dangerous bacteria released into the environment and used in the irrigation of agricultural products, and eventually these bacteria may endanger the human health through foods. Antibiotic-resistant bacteria are mostly found in hospital wastewater. In water and wastewater treatment plants, large amounts of toxic and polluting substances are removed and destroyed, but this process does not eliminate bacteria. Materials and Methods Wastewater samples from 22 hospitals in Iran were collected and in the meantime specific phages (against drug-resistant pathogenic bacteria) extracted using the bilayer agar technique. Phage amplification was performed by employing a fermenter after phage identification. Amplified phages were added to the primary sedimentation pond using New-Brunwick biofermenter BioFlo/Celligen®115 and the bacterial count was evaluated for the desired bacteria. Results Our phage cocktail was able to reduce 99.8%, 99.4%, 99.5%, 99.8%, 99.7%, 99.8%, 99.6% and 99.9% of E. coli, E. faecium, E. faecalis, K. pneumoniae, A. baumannii, P. aeruginosa, S. maltophilia and S. aureus counts respectively. Conclusion The application of phage cocktails can remarkably help improve personal hygiene, the environment, and the optimization of surface water.
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Affiliation(s)
- Sara Sadeqi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Farhad Nikkhahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Javadi
- Department of Community Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Seyed Mahmoud Amin Marashi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
- Corresponding author: Seyed Mahmoud Amin Marashi, Ph.D, Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran. Tel: +98-283-3336001 Fax: +98-283-3324970
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Kambali S, Quinonez E, Sharifi A, Shahraki AH, Kumar N, Dushyantha J, Mirsaeidi M. Pulmonary nontuberculous mycobacterial disease in Florida and association with large-scale natural disasters. BMC Public Health 2021; 21:2058. [PMID: 34758787 PMCID: PMC8579656 DOI: 10.1186/s12889-021-12115-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
Background Little is known about the impact of the ecosystem disruption and its contribution on the non-tuberculosis mycobacteria (NTM) diseases (cases) rate in Florida (FL), a state with a high prevalence of NTM in the United States. We aimed to evaluate the epidemiological distribution of NTM in FL and identify its association with extreme weather events. Methods We used OneFlorida Clinical Research Consortium dataset and extracted data on NTM cases using ICD codes 9- CM 031.0 and ICD-10 A31 during 2012–2018. The number of hurricanes during the study period which affected FL were extracted data from the National Hurricane Center (NHC) and the National Oceanic and Atmospheric Administration (NOAA). Results Prevalence of NTM gradually increased during the study period. The rate was 2012: 14.3/100,000, 2015; 20.1/100,000 and 2018; 22.6/100,00 except in 2014 where there was an 8% decrease. The incidences were 2012; 6.5/100,00, 2015; 4.9/100,000 and in 2015; 5.4/100,000. Geographical analysis demonstrated a gradual expansion of the NTM cases in Alachua, and Marion Counties throughout the study period. Notably, the 2018 heat map showed higher prevalence of NTM in the northwestern, panhandle region of FL which had been absent in the heat maps for years 2012–2018. High number of the hurricanes was associated with the higher number of the new cases of NTM infection for years 2012, 2016–2018, while the lower number of the hurricanes was associated with the lower number of the new cases of NTM infection for years 2014–2015. Conclusion The current study found the prevalence rates of NTM disease in FL rose from 2012 to 2018. A higher prevalence was seen following the hurricanes. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-021-12115-7.
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Affiliation(s)
- Shweta Kambali
- Division of Pulmonary and Critical Care, University of Miami, Miami, Florida, USA
| | - Elena Quinonez
- School of Medicine, University of Miami, Miami, Florida, USA
| | - Arash Sharifi
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, USA
| | - Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, 653-1 8th St West, Jacksonville, Florida, 32209, USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami, Miami, Florida, USA
| | | | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, 653-1 8th St West, Jacksonville, Florida, 32209, USA.
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Shahraki AH, Chaganti SR, Heath D. Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems. BMC Microbiol 2021; 21:253. [PMID: 34548037 PMCID: PMC8454060 DOI: 10.1186/s12866-021-02306-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/25/2020] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02306-y.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Present Address: Cooperative Institute for Great Lakes Research, School of Environmental and Sustainability, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada.
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Sadeghi J, Chaganti SR, Shahraki AH, Heath DD. Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes. Sci Total Environ 2021; 781:146771. [PMID: 33812116 DOI: 10.1016/j.scitotenv.2021.146771] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, SEAS, University of Michigan, Ann Arbor, MI, USA.
| | | | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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15
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Majid Vahed
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mehdi Mirsaeidi
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA; Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL, USA.
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16
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Zhang C, Tian R, Dreifus EM, Hashemi Shahraki A, Holt G, Cai R, Griswold A, Bejarano P, Jackson R, V Schally A, Mirsaeidi M. Activity of the growth hormone-releasing hormone antagonist MIA602 and its underlying mechanisms of action in sarcoidosis-like granuloma. Clin Transl Immunology 2021; 10:e1310. [PMID: 34257968 PMCID: PMC8256670 DOI: 10.1002/cti2.1310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/19/2021] [Revised: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Growth hormone-releasing hormone (GHRH) is a potent stimulator of growth hormone (GH) secretion from the pituitary gland. Although GHRH is essential for the growth of immune cells, the regulatory effects of its antagonist in granulomatous disease remain unknown. METHODS Here, we report expression of GHRH receptor (R) in human tissue with sarcoidosis granuloma and demonstrate the anti-inflammatory effects of MIA602 (a GHRH antagonist) in two in vitro human granuloma models and an in vivo granuloma model using different methods including ELISA, immunohistochemistry, RNA-seq analysis and flow cytometry. RESULTS MIA602 decreases the levels of IL-2, IL-2R, IL-7, IL-12, IL-17A and TNF-α in an in vitro granuloma model. Further, we show that the anti-inflammatory effect of MIA602 appears to be mediated by a reduction in CD45+CD68+ cells in granulomatous tissue and upregulation in PD-1 expression in macrophages. Analysis of the expression of proteins involved in the mitochondrial stage of apoptosis showed that MIA602 increases the levels of caspase-3, BCL-xL/BAK dimer and MCl-1/Bak dimer in the granuloma. These findings indicate that MIA602 may not induce apoptosis. CONCLUSIONS Our findings further suggest that GHRH-R is potentially a clinical target for the treatment of granulomatous disease and that MIA602 may be used as a novel therapeutic agent for sarcoidosis.
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Affiliation(s)
- Chongxu Zhang
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
| | - Runxia Tian
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
| | | | | | - Gregory Holt
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
- Division of Pulmonary and Critical CareUniversity of MiamiMiamiFLUSA
| | - Renzhi Cai
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
| | - Anthony Griswold
- School of MedicineJohn P. Hussman Institute for Human GenomicsUniversity of MiamiMiamiFLUSA
| | | | - Robert Jackson
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
- School of MedicineUniversity of MiamiMiamiFLUSA
| | - Andrew V Schally
- Polypeptide and Cancer InstituteVeterans Affairs Medical CenterMiamiFLUSA
- Department of PathologyUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Mehdi Mirsaeidi
- Section of PulmonaryMiami VA Healthcare SystemMiamiFLUSA
- Division of Pulmonary and Critical CareUniversity of MiamiMiamiFLUSA
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17
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Quinonez E, Vahed M, Hashemi Shahraki A, Mirsaeidi M. Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North America. Viruses 2021; 13:930. [PMID: 34067890 PMCID: PMC8156069 DOI: 10.3390/v13050930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 04/02/2021] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND little is known about the forecasting of new variants of SARS-COV-2 in North America and the interaction of variants with vaccine-derived neutralizing antibodies. METHODS the affinity scores of the spike receptor-binding domain (S-RBD) of B.1.1.7, B. 1.351, B.1.617, and P.1 variants in interaction with the neutralizing antibody (CV30 isolated from a patient), and human angiotensin-converting enzyme 2 (hACE2) receptor were predicted using the template-based computational modeling. From the Nextstrain global database, we identified prevalent mutations of S-RBD of SARS-CoV-2 from December 2019 to April 2021. Pre- and post-vaccination time series forecasting models were developed based on the prediction of neutralizing antibody affinity scores for S-RBD of the variants. RESULTS the proportion of the B.1.1.7 variant in North America is growing rapidly, but the rate will reduce due to high affinity (~90%) to the neutralizing antibody once herd immunity is reached. Currently, the rates of isolation of B. 1.351, B.1.617, and P.1 variants are slowly increasing in North America. Herd immunity is able to relatively control these variants due to their low affinity (~70%) to the neutralizing antibody. The S-RBD of B.1.617 has a 110% increased affinity score to the human angiotensin-converting enzyme 2 (hACE2) in comparison to the wild-type structure, making it highly infectious. CONCLUSION The newly emerged B.1.351, B.1.617, and P.1 variants escape from vaccine-induced neutralizing immunity and continue circulating in North America in post- herd immunity era. Our study strongly suggests that a third dose of vaccine is urgently needed to cover novel variants with affinity scores (equal or less than 70%) to eliminate developing viral mutations and reduce transmission rates.
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Affiliation(s)
- Elena Quinonez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33146, USA;
| | - Majid Vahed
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.V.); (A.H.S.)
| | - Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.V.); (A.H.S.)
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Miami Miller School of Medicine, Miami, FL 33146, USA; (M.V.); (A.H.S.)
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18
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Hashemi Shahraki A, Mirsaeidi M. Phage Therapy for Mycobacterium Abscessus and Strategies to Improve Outcomes. Microorganisms 2021; 9:microorganisms9030596. [PMID: 33799414 PMCID: PMC7999966 DOI: 10.3390/microorganisms9030596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Members of Mycobacterium abscessus complex are known for causing severe, chronic infections. Members of M. abscessus are a new "antibiotic nightmare" as one of the most resistant organisms to chemotherapeutic agents. Treatment of these infections is challenging due to the either intrinsic or acquired resistance of the M. abscessus complex to the available antibiotics. Recently, successful phage therapy with a cocktail of three phages (one natural lytic phage and two engineered phages) every 12 h for at least 32 weeks has been reported against a severe case of the disseminated M. abscessus subsp. massiliense infection, which underlines the high value of phages against drug-resistant superbugs. This report also highlighted the limitations of phage therapy, such as the absence of lytic phages with a broad host-range against all strains and subspecies of the M. abscessus complex and also the risk of phage resistant bacteria over treatment. Cutting-edge genomic technologies have facilitated the development of engineered phages for therapeutic purposes by introducing new desirable properties, changing host-range and arming the phages with additional killing genes. Here, we review the available literature and suggest new potential solutions based on the progress in phage engineering that can help to overcome the present limitations of M. abscessus treatment.
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Shahraki AH, Chaganti SR, Heath DD. Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario. Microb Ecol 2021; 81:1-13. [PMID: 32621209 DOI: 10.1007/s00248-020-01539-0] [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] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
- Cooperative Institute for Great Lakes Research, School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Rohani M, Hashemi Shahraki A, Ghasemi A, Esmaeili S, Karadenizli A, Mostafavi E. The prevalence of Francisella spp. in different natural surface water samples collected from northwest of Iran. IJM 2019. [DOI: 10.18502/ijm.v11i1.699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Francisella tularensis has a wide distribution in northern hemisphere of the world. Up to now, there was little information about the Francisella spp. situation in the environmental samples in Iran. In this study we aimed to determine the prevalence of Francisella spp. in the environmental samples in northwest of Iran.
Materials and Methods: A total of 237 natural water samples from ponds, rivers, lakes, springs and other surface waters from north western provinces of Iran (Kurdistan and Western Azerbaijan) were collected from September to November 2015. All samples were cultured for Francisella and other bacterial species and Real Time TaqMan PCR was performed on the concentrated and DNA extracted samples. For detection of the presence of bacterial DNA in the samples, two different targets in the genome of Francisella, ISFtu2 and fopA were used.
Results: Among the tested surface water samples, 40 (17.09%; 95% CI: 12.67-22.33%) and 12 (5.13%; 95%CI: 2.81-8.56%)
samples were positive for ISFtu2 and fopA respectively. None of them was positive in culture.
Conclusion: The prevalence of Francisella spp. in the environmental samples in the west of Iran is high and it is comparable with Turkey, Iran’s neighboring country. Use of higher copy number genes or IS like ISFtu2 could improve the detection of this organism in the environmental samples.
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21
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Mostafavi E, Molaeipoor L, Esmaeili S, Ghasemi A, Kamalizad M, Yousefi Behzadi M, Naserifar R, Rohani M, Hashemi Shahraki A. Seroprevalence of Q fever among high-risk occupations in the Ilam province, the west of Iran. PLoS One 2019; 14:e0211781. [PMID: 30779802 PMCID: PMC6380538 DOI: 10.1371/journal.pone.0211781] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 01/22/2019] [Indexed: 12/11/2022] Open
Abstract
Background Q fever is a zoonotic disease of great public health importance in Iran. This disease is presented with high phase I antibody development in chronic and high phase II antibody in the acute form of illness. This study was conducted to evaluate the seroprevalence of Q fever among high-risk occupations in the Ilam province in Western Iran. Methods and findings In this cross-sectional study, 367 sera samples were collected from five groups comprised of animal husbandry workers, farmers, butchers, slaughterhouse workers, and park rangers. The collected sera were tested for IgG antibodies against Coxiella burnetii using ELISA. The seroprevalence of antibodies against C. burnetii in phase I and II was 24.38% and 26.37%, respectively (i.e., 32.42% overall). Low educational level, living in rural areas, keeping sheep/goats, ages older than 50 years, and a history of arthropod bites positively correlated with increased risk of Q fever infection. Animal husbandry workers (45.13%) were at higher risk of contracting Q fever compared with other occupations in the study (17.11%). Conclusions High seroprevalence of C. burnetii among high-risk occupations is a serious challenge in the Ilam province. In addition, the high seroprevalence of endemic Q fever in rural and nomadic areas and a higher concentration of occupations who are directly engaged with livestock demonstrate the critical need for preventive medicine education and training in regards to mitigating risk for disease contraction in susceptible groups.
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Affiliation(s)
- Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
- * E-mail:
| | - Leila Molaeipoor
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Saber Esmaeili
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Ghasemi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maedeh Kamalizad
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Manijeh Yousefi Behzadi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Razi Naserifar
- Department of Parasitology, Faculty of Health, Ilam University of Medical Sciences, Ilam, Iran
| | - Mehdi Rohani
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
- Department of Microbiology, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference laboratory for diagnosis and research on Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
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Shahraki AH, Chaganti SR, Heath D. Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities. J Water Health 2019; 17:37-49. [PMID: 30758302 DOI: 10.2166/wh.2018.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail:
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail:
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario N9B 3P4, Canada E-mail: ; Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada
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Rohani M, Shahraki AH, Ghasemi A, Esmaeili S, Karadenizli A, Mostafavi E. The prevalence of Francisella spp. in different natural surface water samples collected from northwest of Iran. Iran J Microbiol 2019; 11:19-24. [PMID: 30996827 PMCID: PMC6462269] [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] [Indexed: 11/03/2022]
Abstract
BACKGROUND AND OBJECTIVES Francisella tularensis has a wide distribution in northern hemisphere of the world. Up to now, there was little information about the Francisella spp. situation in the environmental samples in Iran. In this study we aimed to determine the prevalence of Francisella spp. in the environmental samples in northwest of Iran. MATERIALS AND METHODS A total of 237 natural water samples from ponds, rivers, lakes, springs and other surface waters from north western provinces of Iran (Kurdistan and Western Azerbaijan) were collected from September to November 2015. All samples were cultured for Francisella and other bacterial species and Real Time TaqMan PCR was performed on the concentrated and DNA extracted samples. For detection of the presence of bacterial DNA in the samples, two different targets in the genome of Francisella, ISFtu2 and fopA were used. RESULTS Among the tested surface water samples, 40 (17.09%; 95% CI: 12.67-22.33%) and 12 (5.13%; 95%CI: 2.81-8.56%) samples were positive for ISFtu2 and fopA respectively. None of them was positive in culture. CONCLUSION The prevalence of Francisella spp. in the environmental samples in the west of Iran is high and it is comparable with Turkey, Iran's neighboring country. Use of higher copy number genes or IS like ISFtu2 could improve the detection of this organism in the environmental samples.
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Affiliation(s)
- Mahdi Rohani
- Department of Microbiology, Pasteur Institute of Iran, Tehran, Iran,National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Abdolrazagh Hashemi Shahraki
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Ghasemi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran,Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saber Esmaeili
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran,Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Aynur Karadenizli
- Department of Medical Microbiology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Ehsan Mostafavi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Ehsan Mostafavi, Ph.D, National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran; Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran. Tel: +98-21-6411212, Fax: +98-21-89776655,
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Khosravi AD, Hashemzadeh M, Hashemi Shahraki A, Teimoori A. Differential Identification of Mycobacterial Species Using High-Resolution Melting Analysis. Front Microbiol 2017; 8:2045. [PMID: 29109708 PMCID: PMC5660063 DOI: 10.3389/fmicb.2017.02045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 07/13/2017] [Accepted: 10/06/2017] [Indexed: 01/20/2023] Open
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) is increasing wordwide. Due to the difference in treatment of NTM infections and tuberculosis, rapid species identification of mycobacterial clinical isolates is necessary for the effective management of mycobacterial diseases treatment and their control strategy. In this study, a cost-effective technique, real-time PCR coupled with high-resolution melting (HRM) analysis, was developed for the differentiation of Mycobacterial species using a novel rpoBC sequence. A total of 107 mycobacterial isolates (nine references and 98 clinical isolates) were subjected to differentiation using rpoBC locus sequence in a real-time PCR-HRM assay scheme. From 98 Mycobacterium clinical isolates, 88 species (89.7%), were identified at the species level by rpoBC locus sequence analysis as a gold standard method. M. simiae was the most frequently encountered species (41 isolates), followed by M. fortuitum (20 isolates), M. tuberculosis (15 isolates), M. kansassi (10 isolates), M. abscessus group (5 isolates), M. avium (5 isolates), and M. chelonae and M. intracellulare one isolate each. The HRM analysis generated six unique specific groups representing M. tuberculosis complex, M. kansasii, M. simiae, M. fortuitum, M. abscessus–M. chelonae group, and M. avium complex. In conclusion, this study showed that the rpoBC-based real-time PCR followed by HRM analysis could differentiate the majority of mycobacterial species that are commonly encountered in clinical specimens.
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Affiliation(s)
- Azar D Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Hashemi Shahraki A, Trovato A, Droz S, Haidarieh P, Borroni E, Mirsaeidi M, Mannino R, Hashemzadeh M, Mariottini A, Cirillo DM, Tortoli E. Mycobacterium aquaticum sp. nov., a rapidly growing species isolated from haemodialysis water. Int J Syst Evol Microbiol 2017; 67:3279-3282. [PMID: 28829035 DOI: 10.1099/ijsem.0.002103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The characterization of five Iranian isolates, four from hospital haemodialysis water and one from the sputum of a patient, led to the detection of a novel mycobacterium species. The strains were characterized by mucoid colonies developing in 3-5 days at temperatures ranging from 25 to 37 °C. The biochemical test pattern was unremarkable while the HPLC profile of mycolic acids resembled that of Mycobacterium fortuitum. The sequences of three major housekeeping genes (16S rRNA, hsp65 and rpoB) were unique and differed from those of any other mycobacterium. Mycobacterium brisbanense, which is the species that shared the highest 16S rRNA gene sequence similarity (99.03 %), was distinct, as shown by the average nucleotide identity and by the genome to genome distance values (91.05 and 43.10 %, respectively). The strains are thus considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium aquaticum sp. nov. is proposed. The type strain is RW6T (=DSM 104277T=CIP111198T).
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Affiliation(s)
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Sara Droz
- Institute for Infectious Diseases, University of Berne, Berne, Switzerland
| | - Parvin Haidarieh
- Department of Microbiology, School of Medicine, Alborz University, Karaj, Iran
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University Miami, Miami, FL, USA
| | - Roberta Mannino
- Microbiology and Virology Laboratory, Careggi University Hospital, Firenze, Italy
| | - Mohamad Hashemzadeh
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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Khosravi AD, Shahraki AH, Dezfuli SK, Hashemzadeh M, Goodarzi H, Mohajeri P. Genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains isolated from tuberculosis patients in Iran using MIRU-VNTR technique. Kaohsiung J Med Sci 2017; 33:550-557. [PMID: 29050672 DOI: 10.1016/j.kjms.2017.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 01/23/2017] [Revised: 06/13/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is considered as one of the most important infectious diseases in the world, and recent rise and spread of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains, have made the matter worsened. Due to the importance of TB prevalence in Iran, this study was designed to investigate the genetic diversity among MDR strains of MTB by MIRU-VNTR typing scheme. A total of 88 drug resistant M. tuberculosis isolates belong to pulmonary TB cases were collected from several TB reference centers of Iran. Drug susceptibility testing for Isoniazid and Rifampin was performed using the agar proportion method and MDR isolates were underwent genotyping by using 12-locus- based MIRU-VNTR typing. On performing proportion method, 22 isolates were identified as MDR. By typing of MDR isolates using 12-loci MIRU-VNTR technique, high diversity were demonstrated in MDR strains and these were classified into 20 distinct MIRU-VNTR genotypes. MIRU loci 10 and 26 were the most discriminatory loci with 8 and 7 alleles respectively; while MIRU loci 2, 20, 24 and 39 were found to be the least discriminatory with 1-2 alleles each. We noticed a mixed infection in isolate 53, as this isolate comprised simultaneous two alleles in MIRU loci 40, 10, 16 and 39. In conclusion, this result represents MIRU-VNTR typing as a useful tool for studying genetic diversity of MDR-MTB in regional settings, and will help the health sectors to construct a preventive program for MDR-TB. Additionally, it can detect mixed infection which can facilitate management of treatment.
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Affiliation(s)
- Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Soolmaz Khandan Dezfuli
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamed Goodarzi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parviz Mohajeri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Shahraki AH, Trovato A, Mirsaeidi M, Borroni E, Heidarieh P, Hashemzadeh M, Shahbazi N, Cirillo DM, Tortoli E. Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri. Int J Syst Evol Microbiol 2017. [PMID: 28629501 DOI: 10.1099/ijsem.0.001862] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.
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Affiliation(s)
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Parvin Heidarieh
- Department of Microbiology and Immunology, Alborz University of Medical Science, Karaj, Iran
| | - Mohamad Hashemzadeh
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Narges Shahbazi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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Dastranj M, Farahani A, Hashemi Shahraki A, Atashi S, Mohajeri P. Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran. Clin Respir J 2017; 12:996-1002. [PMID: 28224727 DOI: 10.1111/crj.12617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 02/13/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND AIMS Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis. METHODS A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification. RESULTS A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%). CONCLUSIONS The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.
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Affiliation(s)
- Mahsa Dastranj
- Microbiology Department, Kurdistan Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Abbas Farahani
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Sara Atashi
- West Tuberculosis Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parviz Mohajeri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Shirudi Shahid Boulevard, Daneshgah Street, Kermanshah, 67148-69914, Iran
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Mostafavi E, Shahraki AH, Japoni-Nejad A, Esmaeili S, Darvish J, Sedaghat MM, Mohammadi A, Mohammadi Z, Mahmoudi A, Pourhossein B, Ghasemi A, Gyuranecz M, Carniel E. A Field Study of Plague and Tularemia in Rodents, Western Iran. Vector Borne Zoonotic Dis 2017; 17:247-253. [PMID: 28165869 DOI: 10.1089/vbz.2016.2053] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 12/18/2022] Open
Abstract
INTRODUCTION Kurdistan Province in Iran is a historical focus for plague and tularemia. This study aimed at assessing the current status of these two foci by studying their rodent reservoirs. MATERIALS AND METHODS Rodents were trapped and their ectoparasites were collected. The genus and species of both rodents and ectoparasites were determined. Serological analyses of rodent blood samples were done by enzyme-linked immunosorbent assay for plague and by standard tube agglutination assay for tularemia. Rodent spleen samples were subjected to bacterial culture, microscopic examination, and real-time PCR to search for active plague or tularemia infection. RESULTS During this study, 245 rodents were trapped, of which the most abundant genera were Apodemus (40%), Mus (24.49%), and Meriones (12.65%). One hundred fifty-three fleas, 37 mites, and 54 ticks were collected on these rodents. The results of all direct and indirect tests were negative for plague. Serological tests were positive for tularemia in 4.8% of trapped rodents. DISCUSSION This study is the first report on the presence of tularemia infection in rodents in Western Iran. Since Meriones persicus is a known reservoir for plague and tularemia, and this rodent carried plague and tularemia vectors in Marivan and Sanandaj districts, there is a real potential for the occurrence of these two diseases in this region.
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Affiliation(s)
- Ehsan Mostafavi
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,2 Department of Epidemiology and Biostatistics, Pasteur Institute of Iran , Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,2 Department of Epidemiology and Biostatistics, Pasteur Institute of Iran , Tehran, Iran
| | - Alireza Japoni-Nejad
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran
| | - Saber Esmaeili
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,2 Department of Epidemiology and Biostatistics, Pasteur Institute of Iran , Tehran, Iran .,3 Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran, Iran
| | - Jamshid Darvish
- 4 Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad , Mashhad, Iran
| | | | - Ali Mohammadi
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,5 School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zeinolabedin Mohammadi
- 4 Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad , Mashhad, Iran
| | - Ahmad Mahmoudi
- 4 Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad , Mashhad, Iran
| | - Behzad Pourhossein
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,2 Department of Epidemiology and Biostatistics, Pasteur Institute of Iran , Tehran, Iran .,6 Department of Virology, School of Public Health, Tehran University of Medical Sciences , Tehran, Iran
| | - Ahmad Ghasemi
- 1 Research Centre for Emerging and Reemerging Infectious Diseases, National Reference Laboratory of Plague, Tularemia and Q Fever, Pasteur Institute of Iran , Kabudar Ahang, Hamadan, Iran .,2 Department of Epidemiology and Biostatistics, Pasteur Institute of Iran , Tehran, Iran .,3 Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran, Iran
| | - Miklós Gyuranecz
- 7 Institute for Veterinary Medical Research , Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Elisabeth Carniel
- 8 Yersinia Research Unit, National Reference Laboratory, WHO Collaborating Center for Yersinia , Institut Pasteur, Paris, France
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Ghasemi A, Esmaeili S, Hashemi Shahraki A, Hanifi H, Mohammadi Z, Mahmoudi A, Rohani M, Mostafavi E. Upsurge of Rodents’ Population in a Rural Area of Northeastern Iran Raised Concerns about Rodent-borne Diseases. JoMMID 2017. [DOI: 10.29252/jommid.5.1.2.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Mohajeri P, Yazdani L, Shahraki AH, Alvandi A, Atashi S, Farahani A, Almasi A, Rezaei M. Verification of Frequency in Species of Nontuberculous Mycobacteria in Kermanshah Drinking Water Supplies Using the PCR-Sequencing Method. Microb Drug Resist 2016; 23:359-364. [PMID: 27668545 DOI: 10.1089/mdr.2016.0064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 11/12/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacteria are habitants of environment, especially in aquatic systems. Some of them cause problems in immunodeficient patients. Over the last decade, 16S rRNA gene sequencing was established in 45 novel species of nontuberculous mycobacteria. Experiences revealed that this method underestimates the diversity, but does not distinguish between some of mycobacterium subsp. To recognize emerging rapidly growing mycobacteria and identify their subsp, rpoB gene sequencing has been developed. OBJECTIVES To better understand the transmission of nontuberculous mycobacterial species from drinking water and preventing the spread of illness with these bacteria, the aim of this study was to detect the presence of bacteria by PCR-sequencing techniques. MATERIALS AND METHODS Drinking water samples were collected from different areas of Kermanshah city in west of IRAN. After decontamination with cetylpyridinium chloride, samples were filtered with 0.45-micron filters, the filter transferred directly on growth medium waiting to appear in colonies, then DNA extraction and PCR were performed, and products were sent to sequencing. RESULTS We found 35/110 (32%) nontuberculous mycobacterial species in drinking water samples, isolates included Mycobacterium goodii, Mycobacterium aurum, and Mycobacterium gastri with the most abundance (11.5%), followed by Mycobacterium smegmatis, Mycobacterium porcinum, Mycobacterium peregrinum, Mycobacterium mucogenicum, and Mycobacterium chelonae (8%). CONCLUSIONS In this study, we recognized the evidence of contamination by nontuberculous mycobacteria in corroded water pipes. As a result of the high prevalence of these bacteria in drinking water in Kermanshah, this is important evidence of transmission through drinking water. This finding can also help public health policy makers control these isolates in drinking water supplies in Kermanshah.
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Affiliation(s)
- Parviz Mohajeri
- 1 Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Laya Yazdani
- 1 Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | | | - Amirhoshang Alvandi
- 1 Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Sara Atashi
- 3 West Tuberculosis Center, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Abbas Farahani
- 4 Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Ali Almasi
- 5 Department of Environmental Health, Public Health College, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Mansour Rezaei
- 6 Department of Biostatistics, Faculty of Medicine, Kermanshah University of Medical Sciences , Kermanshah, Iran
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Abstract
Leptospirosis is a zoonosis and a major public health problem. Blood sampling was done in the province of Kurdistan from 250 members of different groups, including hunters and their families, butchers and slaughterhouse workers, healthcare workers (HCWs) and those referred to medical diagnostic laboratories for routine testing. Sera were tested using an ELISA method to detect specific Leptsopira IgG antibodies. We found 20.80% (95% confidence interval, 16.23-26.25%) to be positive. The highest and lowest seroprevalence were in hunters (26%) and HCWs (18%). There was significant positive correlation between age and seropositivity ( P = 0.01). Hunting and eating the meat of the hare and exposure to dead or dying wild animals were found to be the main risk factors ( P < 0.05).
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Affiliation(s)
- Saber Esmaeili
- 1 Researcher, Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- 2 Researcher, National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
- 3 PhD Student, Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- 4 Associate Professor, Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- 5 Head of Laboratory, National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Fahimeh Bagheri Amiri
- 6 Researcher, Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- 7 PhD, Department of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mohammad Karimi
- 8 Responsible of Communicable Diseases Control, Deputy of Health, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ehsan Mostafavi
- 9 Associate Professor and Head of Department, Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- 10 Head of Center, National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
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Abstract
OBJECTIVES: Plague remains a public health concern worldwide, particularly in old foci. Multiple epidemics of this disease have been recorded throughout the history of Iran. Despite the long-standing history of human plague in Iran, it remains difficult to obtain an accurate overview of the history and current status of plague in Iran. METHODS: In this review, available data and reports on cases and outbreaks of human plague in the past and present in Iran and in neighboring countries were collected, and information was compiled regarding when, where, and how many cases occurred. RESULTS: This paper considers the history of plague in Persia (the predecessor of today’s Iran) and has a brief review of plague in countries in the World Health Organization Eastern Mediterranean Region, including a range of countries in the Middle East and North Africa. CONCLUSIONS: Since Iran has experienced outbreaks of plague for several centuries, neighboring countries have reported the disease in recent years, the disease can be silent for decades, and the circulation of Yersinia pestis has been reported among rodents and dogs in western Iran, more attention should be paid to disease monitoring in areas with previously reported human cases and in high-risk regions with previous epizootic and enzootic activity.
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Affiliation(s)
- Abdolrazagh Hashemi Shahraki
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,National Reference Laboratory for Plague, Tularemia, and Q fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Elizabeth Carniel
- Yersinia Research Unit, National Reference Laboratory, Institut Pasteur, Paris, France
| | - Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,National Reference Laboratory for Plague, Tularemia, and Q fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
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Mostafavi E, Nasehi M, Hashemi Shahraki A, Esmaeili S, Ghaderi E, Sharafi S, Doosti-Irani A. Comparison of the tuberculin skin test and the QuantiFERON-TB Gold test in detecting latent tuberculosis in health care workers in Iran. Epidemiol Health 2016; 38:e2016032. [PMID: 27457062 PMCID: PMC5037355 DOI: 10.4178/epih.e2016032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 07/08/2016] [Accepted: 07/24/2016] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES: The tuberculin skin test (TST) and the QuantiFERON-TB Gold test (QFT) are used to identify latent tuberculosis infections (LTBIs). The aim of this study was to determine the agreement between these two tests among health care workers in Iran. METHODS: This cross-sectional study included 177 tuberculosis (TB) laboratory staff and 67 non-TB staff. TST indurations of 10 mm or more were considered positive. The Student’s t-test and the chi-square test were used to compare the mean score and proportion of variables between the TB laboratory staff and the non-TB laboratory staff. Kappa statistics were used to evaluate the agreement between these tests, and logistic regression was used to assess the risk factors associated with positive results for each test. RESULTS: The prevalence of LTBIs according to both the QFT and the TST was 17% (95% confidence interval [CI], 12% to 21%) and 16% (95% CI, 11% to 21%), respectively. The agreement between the QFT and the TST was 77.46%, with a kappa of 0.19 (95% CI, 0.04 to 0.34). CONCLUSIONS: Although the prevalence of LTBI based on the QFT and the TST was not significantly different, the kappa statistic was low between these two tests for the detection of LTBIs.
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Affiliation(s)
- Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Mahshid Nasehi
- Center for Diseases Control and Prevention, Ministry of Health and Medical Education, Tehran, Iran.,Department of Epidemiology and Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran
| | - Saber Esmaeili
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar-Ahang, Hamadan, Iran.,Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ebrahim Ghaderi
- Social Determinants of Health Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Department of Epidemiology and Biostatistics, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Saeed Sharafi
- Center for Diseases Control and Prevention, Ministry of Health and Medical Education, Tehran, Iran
| | - Amin Doosti-Irani
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran.,Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Sadeghi P, Khosravi AD, Hashemi Shahraki A, Beiranvand M. Identification of clinical isolates of Acinetobacter baumannii from Iran and study of their heterogeneity. J Chin Med Assoc 2016; 79:382-6. [PMID: 27053435 DOI: 10.1016/j.jcma.2016.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 12/17/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii has become one of the most serious causative agents of nosocomial infections due to its significant ability to survive on hospital surfaces. It is mainly an emerging opportunistic pathogen infecting patients in intensive care units. This study was aimed to identify the clinical isolates of A. baumannii and to investigate their heterogeneity using polymerase chain reaction (PCR)-based typing methods. METHODS A total of 197 nonduplicate isolates recovered from a wide range of clinical samples were subjected to conventional cultural and biochemical tests. For those isolates that were preliminary identified as A. baumannii, rpoB-based PCR with subsequent restriction fragment length polymorphism (RFLP) using two restriction enzymes (TagI and HaeIII) was performed to investigate the genetic diversity of the strains and their presumptive relationships with different clinical presentation of the disease caused by this pathogen. RESULTS In total, 50 isolates (25.4%) were identified as A. baumannii using conventional phenotypic methods with subsequent confirmation by rpoB sequencing. RFLP analysis demonstrated five different restriction enzyme patterns, designated as A-E clusters. Most A. baumannii isolates were categorized under Cluster A (32%). We found no significant relationship between clinical presentation and the clustering of the isolates. CONCLUSION This study showed that the rpoB region possesses high discriminatory power to identify the isolates to the species level. This marker showed high interspecies variability that might be useful for strain typing. The results also suggest the possibility of the existence of a predominant clone of A. baumannii among infected patients in Iran.
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Affiliation(s)
- Parisa Sadeghi
- Clinical Biochemistry Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran; Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Abdolrazagh Hashemi Shahraki
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; International Network, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Beiranvand
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Rezaei F, Haeili M, Mohajeri P, Hashemi Shahraki A, Imani Fooladi AA, Zahednamazi F, Feizabadi MM. Frequency of mutational changes in the embB among the ethambutol-resistant strains of Mycobacterium tuberculosis in Iran. J Infect Dev Ctries 2016; 10:363-8. [PMID: 27130997 DOI: 10.3855/jidc.7215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/06/2015] [Accepted: 10/14/2015] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Early detection of drug resistant tuberculosis is one of the main priorities of TB control program. Ethambutol (EMB) is a first-line anti-TB drug that is effective for preventing treatment failures caused by Mycobacterium tuberculosis strains that are resistant to other drugs. The aim of this study was to sequence the embB gene to characterize the mutations causing resistance to EMB and to analyze the relationship between bacterial genotype and EMB resistance among M. tuberculosis isolates in Iran. METHODOLOGY A total of 20 M. tuberculosis isolates comprising 10 multidrug-resistant (MDR) and 10 non-MDR isolates, recovered from TB patients in four regions: Tehran, Isfahan, Zahedan, Khorasan, were analyzed. Mutational profiling was performed by amplifying and sequencing the embB gene. Spoligotyping was carried out to characterize the bacterial genotype. RESULTS Phenotypic EMB resistance was found in 13 strains. Mutations affecting ethambutol resistance-determining region (ERDR) of the embB were identified in 6 of 13 EMB-resistant isolates. The majority of these mutations resulted in amino acid substitution at position 306 (M306V). A novel mutation at codon 366 was identified (S366L) in one isolate. Ural was the most predominant genotype in the studied population. Beijing genotype was associated with both MDR and EMB resistance in which all mutations occurred at codon 306 of the embB gene. CONCLUSION A significant association between Beijing genotype and EMB resistance was found, mainly due to mutations at embB306. Results of this study can be used as a basis to develop or improve rapid molecular tests to monitor drug-resistant strains in this country.
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Affiliation(s)
- Faranak Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Khosravi AD, Hashemi Shahraki A, Hashemzadeh M, Sheini Mehrabzadeh R, Teimoori A. Prevalence of Non-Tuberculous Mycobacteria in Hospital Waters of Major Cities of Khuzestan Province, Iran. Front Cell Infect Microbiol 2016; 6:42. [PMID: 27148491 PMCID: PMC4829604 DOI: 10.3389/fcimb.2016.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 01/21/2016] [Accepted: 03/26/2016] [Indexed: 11/13/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are among the emerging pathogens in immunocompromised individuals including hospitalized patients. So, it is important to consider hospitals water supplies as a source for infection. The aim of this study was to determine the prevalence of NTM in the hospital aquatic systems of Khuzestan, South west of Iran. In total, 258 hospital water samples were collected and examined. After initial sample processing, sediment of each sample were inoculated into two Lowenstein-Jensen medium. The positive cultures were studied with phenotypic tests including growth rate, colony morphology, and pigmentation, with subsequent PCR- restriction enzyme analysis (PRA) and rpoB gene sequence analysis. Mycobacterial strains were isolated from 77 samples (29.8%), comprising 52 (70.1%) rapid growing, and 25 (32.4%) slow growing mycobacteria. Based on the overall results, M. fortuitum (44.1%) was the most common mycobacterial species in hospital water samples, followed by M. gordonae (n = 13, 16.8%) and M. senegalense (n = 5, 7.7%). In conclusion, current study demonstrated the NTM strains as one of the major parts of hospital water supplies with probable potential source for nosocomial infections. This finding also help to shed light on to the dynamics of the distribution and diversity of NTM in the water system of hospitals in the region of study.
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Affiliation(s)
- Azar Dokht Khosravi
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Abdolrazagh Hashemi Shahraki
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Department of Epidemiology, Pasteur Institute of IranTehran, Iran
| | - Mohammad Hashemzadeh
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Rasa Sheini Mehrabzadeh
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Ali Teimoori
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical ScienceAhvaz, Iran
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Esmaeili S, Naddaf SR, Pourhossein B, Hashemi Shahraki A, Bagheri Amiri F, Gouya MM, Mostafavi E. Seroprevalence of Brucellosis, Leptospirosis, and Q Fever among Butchers and Slaughterhouse Workers in South-Eastern Iran. PLoS One 2016; 11:e0144953. [PMID: 26731333 PMCID: PMC4701462 DOI: 10.1371/journal.pone.0144953] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/25/2015] [Indexed: 01/25/2023] Open
Abstract
Zoonotic diseases can be occupational hazards to people who work in close contact with animals or their carcasses. In this cross-sectional study, 190 sera were collected from butchers and slaughterhouse workers in different regions of the Sistan va Baluchestan province, in Iran in 2011. A questionnaire was filled for each participant to document personal and behavioural information. The sera were tested for detection of specific IgG antibodies against brucellosis, leptospirosis, and Q fever (phase I and II) using commercial enzyme-linked immunosorbent assays (ELISA). The seroprevalence of brucellosis was 7.9%, leptospirosis 23.4%, and phase I and II of Q fever were 18.1% and 14.4%, respectively. The seroprevalence of Q fever and leptospirosis, but not brucellosis, varied among regions within the province (p = 0.01). Additionally, a significant relationship was found between seropositivity of Q fever and camel slaughtering (p = 0.04). Reduced seropositivity rate of brucellosis was associated with use of personal protective equipment (PPE) (p = 0.004). This study shows that brucellosis, leptospirosis and Q fever occur among butchers and slaughterhouse workers in this area.
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Affiliation(s)
- Saber Esmaeili
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q fever, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Behzad Pourhossein
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q fever, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Fahimeh Bagheri Amiri
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- Department of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | | | - Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q fever, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
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Kardan Yamchi J, Haeili M, Gizaw Feyisa S, Kazemian H, Hashemi Shahraki A, Zahednamazi F, Imani Fooladi AA, Feizabadi MM. Evaluation of efflux pump gene expression among drug susceptible and drug resistant strains of Mycobacterium tuberculosis from Iran. Infect Genet Evol 2015; 36:23-26. [PMID: 26325681 DOI: 10.1016/j.meegid.2015.08.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 05/29/2015] [Revised: 08/18/2015] [Accepted: 08/26/2015] [Indexed: 11/18/2022]
Abstract
Absence of mutations within the genes encoding drug targets in some phenotypically drug resistant strains of Mycobacterium tuberculosis suggests possible involvement of alternative mechanisms such as over-expression of efflux pumps. We investigated the expression level of Rv1410c, Rv2459, Rv1218c and Rv1273c efflux pumps gene by real-time quantitative reverse transcription PCR (qRT-PCR) in 31 clinical isolates of M. tuberculosis. Susceptibility to first-line drugs was performed using the proportion method. Twenty one isolates were characterized with drug resistance (DR), and among them 12 showed a significantly elevated level of expression (>4 fold) for at least one of the studied genes encoding for efflux pumps. Point mutations in the katG (codons 315 or 335) and rpoB (codons 456 and 441) genes were found in 42.85% and 66.6% of drug resistant isolates, respectively. Only one isolate showed mutation at position -15 of the inhA promoter region. Among the 7 isolates (33.33%) which had no mutation in the studied regions of drug target genes, 5 isolates showed over-expression for efflux pumps. Our results demonstrated that over-expression of efflux pumps can contribute to drug resistance in M. tuberculosis.
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Affiliation(s)
- Jalil Kardan Yamchi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehri Haeili
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Seifu Gizaw Feyisa
- Tehran University of Medical Sciences, International Campus (TUMS-IC), Tehran, Iran
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Zahednamazi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Khosravi AD, Sadeghi P, Shahraki AH, Heidarieh P, Sheikhi N. Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes. J Clin Diagn Res 2015; 9:DC09-13. [PMID: 26393127 DOI: 10.7860/jcdr/2015/13867.6188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 03/06/2015] [Accepted: 05/04/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND Acinetobacter spp. is a diverse group of Gram-negative bacteria which are ubiquitous in soil and water, and an important cause of nosocomial infections. The purpose of this study was to identify a collection of Acinetobacter spp. clinical isolates accurately and to investigate their antibiotic susceptibility patterns. MATERIALS AND METHODS A total of 197 non-duplicate clinical isolates of Acinetobacter spp. isolates identified using conventional biochemical tests. The molecular technique of PCR-RFLP and sequence analysis of rpoB and 16S rRNA genes was applied for species identification. Antimicrobial susceptibility test was performed with a disk diffusion assay. RESULTS Based on 16S rRNA and rpoB genes analysis separately, most of clinical isolates can be identified with high bootstrap values. However, the identity of the isolate 555T was uncertain due to high similarity of A. grimontii and A. junii. Identification by concatenation of 16S rRNA and rpoB confirmed the identity of clinical isolates of Acenitobacer to species level confidently. Accordingly, the isolate 555T assigned as A. grimontii due to 100% similarity to A. grimontii. Moreover, this isolate showed 98.64% to A. junii. Besides, the identity of the isolates 218T and 364T was confirmed as Genomic species 3 and A. calcoaceticus respectively. So, the majority of Acinetobacter spp. isolates, were identified as: A. baumannii (131 isolates, 66%), A. calcoaceticus (9 isolates, 4.5%), and A. genomosp 16 (8 isolates, 4%). The rest of identified species showed the lower frequencies. In susceptibility test, 105 isolates (53%), presented high antibiotic resistance of 90% to ceftriaxone, piperacillin, piperacillin tazobactam, amikacin, and 81% to ciprofloxacin. CONCLUSION Sequence analysis of the 16S rRNA and rpoB spacer simultaneously was able to do identification of Acinetobacter spp. to species level. A.baumannii was identified as the most prevalent species with high antibiotic resistance. Other species showed lower frequencies ranged from 4 to 9 strains.
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Affiliation(s)
- Azar Dokht Khosravi
- Professor, Department of Microbiology & Health Research Institute, School of Medicine, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Parisa Sadeghi
- Research Assistant, Department of Microbiology, School of Medicine, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran; Clinical Biochemistry Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Abdolrazagh Hashemi Shahraki
- Assistant Professor, Department of Health Research Institute, School of Medicine, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran; Department of Epidemiology, Pasteur Institute of Iran
| | - Parvin Heidarieh
- Assistant Professor, Department of Bacteriology and Virology, Alborz University of Medical Sciences , Karaj, Iran
| | - Nasrin Sheikhi
- Research Assistant, Department of Microbiology Unit, Masoud Medical Laboratory , Tehran, Iran
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Nasiri MJ, Dabiri H, Darban-Sarokhalil D, Hashemi Shahraki A. Prevalence of Non-Tuberculosis Mycobacterial Infections among Tuberculosis Suspects in Iran: Systematic Review and Meta-Analysis. PLoS One 2015; 10:e0129073. [PMID: 26052701 PMCID: PMC4460155 DOI: 10.1371/journal.pone.0129073] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/04/2015] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION The infections due to Non-Tuberculosis Mycobacteria (NTM) are becoming an important health problem in many countries in the world. Globally, an increase in NTM infections has been reported from many countries around the world. However, limited information is available about the prevalence of NTM infections in Iran. MATERIAL AND METHODS The data of the prevalence of NTM infections were collected from databases such as PubMed, Web of science, Cochrane Library, Embase, Scopus, Iranmedex, and Scientific Information Database. Comprehensive Meta-Analysis (V2.0, Biostat) software was used to analyze the data. RESULTS The meta-analyses showed that the prevalence of NTM infections was 10.2% (95% confidence interval [95% CI] 6.3-15.9) among culture-positive cases of tuberculosis (TB) in Iran. The further stratified analyses indicated that the prevalence of NTM was higher in studies that were done after year 2000. Additionally, M. simiae (43.3% [95% CI 36.8-50.0]), M. intracellucar (27.3% [95% CI 0.7-95.5]) and M. fortuitum (22.7% [95% CI 16.1-30.9]) were the most prevalent NTM species, respectively. DISCUSSION The relatively high prevalence of NTM infections (10.2%) among culture positive cases for TB underlines the need for greater enforcement of infection control strategies. Establishment of appropriate diagnostic criteria and management guidelines for NTM diseases and expanding the number and quality of regional reference laboratories may facilitate more accurate action for prevention and control of NTM infections in Iran.
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Affiliation(s)
- Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- * E-mail:
| | - Hossein Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Shahraki AH, Heidarieh P, Bostanabad SZ, Khosravi AD, Hashemzadeh M, Khandan S, Biranvand M, Schraufnagel DE, Mirsaeidi M. "Multidrug-resistant tuberculosis" may be nontuberculous mycobacteria. Eur J Intern Med 2015; 26:279-84. [PMID: 25784643 PMCID: PMC4414892 DOI: 10.1016/j.ejim.2015.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Multidrug resistant tuberculosis (MDR-TB) presents a great challenge to public health, especially for developing countries. Some nontuberculous mycobacteria (NTM) cause the similar clinical and radiological characteristics with tuberculosis. We aimed to identify the frequency of NTM infections among subjects who were suspected to have MDR-TB due to lack of response to anti-TB treatment. METHODS This retrospective study evaluated patients with suspected MDR-TB due to lack of sputum conversion after 2-3 month therapy with first line anti-TB treatment from 2009 through 2014. Cultures for mycobacteria were performed and identification was done to species level by phenotypic and molecular tests. The outcome of the patients with NTM disease and related risk factors for poor outcome were evaluated. RESULTS Out of 117 consecutive strains isolated from suspected MDR-TB subjects, 35 (30%) strains were identified as NTM by using conventional and molecular approaches. Of these patients with positive NTM cultures, 32 (27%) patients met ATS/IDSA diagnostic criteria. Out of 32, 29 (90%) individuals with confirmed NTM diseases had underlying disorders including 8 subjects with malignancy, 5 with organ transplantations, and 4 with the human immunodeficiency virus. No known underlying disorder was found in 3 (9%) subjects. Treatment outcomes were available for 27 subjects, 17 (63%) of whom were cured and 10 (37%) had poor outcome including 6 (60%) who failed and 4 (40%) who died during treatment. CONCLUSION The high costs to the patient and society should lead health care providers to consider NTM in all patients suspected of having TB.
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Affiliation(s)
| | - Parvin Heidarieh
- Department of Microbiology, Alborz University of Medical Science, Karaj, Iran
| | - Saeed Zaker Bostanabad
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azar Dokht Khosravi
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Solmaz Khandan
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Biranvand
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Dean E Schraufnagel
- Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL, USA
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Illinois at Chicago, Chicago, IL, USA.
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Kazemian H, Haeili M, Kardan Yamchi J, Rezaei F, Gizaw Feyisa S, Zahednamazi F, Mohajeri P, Zaker Bostanabd S, Hashemi Shahraki A, Imani Fooladi AA, Feizabadi MM. Antimycobacterial activity of linezolid against multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis in Iran. Int J Antimicrob Agents 2015; 45:668-70. [PMID: 25795315 DOI: 10.1016/j.ijantimicag.2015.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehri Haeili
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Jalil Kardan Yamchi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faranak Rezaei
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seifu Gizaw Feyisa
- Tehran University of Medical Sciences, International Campus (TUMS-IC), Tehran, Iran
| | - Fatemeh Zahednamazi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Parviz Mohajeri
- Department of Microbiology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Zaker Bostanabd
- Department of Mycobacteriology, Masoud Medical Laboratory, Mirdamad Street, Tehran, Iran
| | | | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Shahraki AH, Çavuşoğlu C, Borroni E, Heidarieh P, Koksalan OK, Cabibbe AM, Hashemzadeh M, Mariottini A, Mostafavi E, Cittaro D, Feizabadi MM, Lazarevic D, Yaghmaei F, Molinari GL, Camaggi A, Tortoli E. Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens. Int J Syst Evol Microbiol 2014; 65:510-515. [PMID: 25389151 DOI: 10.1099/ijs.0.064832-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5-96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207(T) ( = DSM 46765(T) = JCM 18439(T)).
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Affiliation(s)
| | - Cengiz Çavuşoğlu
- Department of Medical Microbiology, Ege University, Izmir, Turkey
| | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, Alborz University of Medical Science, Karaj, Iran
| | - Orhan Kaya Koksalan
- Institute for Medical Experimental Research, Istanbul University, Istanbul, Turkey
| | | | - Mohamad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Ehsan Mostafavi
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Farhad Yaghmaei
- Department of Epidemiology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Anna Camaggi
- Microbiology Laboratory, Ospedale Maggiore Carità, Novara, Italy
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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