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Khosravi AD, Meghdadi H, Hashemzadeh M, Alami A, Tabandeh MR. Application of a new designed high resolution melting analysis for mycobacterial species identification. BMC Microbiol 2024; 24:205. [PMID: 38851713 PMCID: PMC11161915 DOI: 10.1186/s12866-024-03361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
The Non-tuberculous mycobacterial (NTM) isolates should be distinguished from tuberculosis and identified at the species level for choosing an appropriate treatment plan. In this study, two molecular methods were used to differentiate NTM species, including a new designed High Resolution Melting (HRM) and Multilocus Sequence Analysis (MLSA). Seventy-five mycobacterial isolates were evaluated by sequencing four genes ( MLSA) and a HRM assay specifically targeting atpE was designed to rapidly and accurately identify and differentiate mycobacterium species. Out of 70 NTM isolates, 66 (94.3%), 65 (92.9%), 65 (92.9%) and 64 (91.4%) isolates were identified to the species level by PCR of atpE, tuf, rpoB and dnaK genes. We could identify 100% of the isolates to the species level (14 different species) by MLSA. By using HRM assay, all NTM isolates were identified and classified into eight groups, in addition, Mycobacterium tuberculosis and Nocardia were also detected simultaneously. The MLSA technique was able to differentiate all 14 species of NTM isolates. According to the results, the HRM assay is a rapid and beneficial method for identifying NTM, M. tuberculosis (MTB), and Nocardia isolates without sequencing.
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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, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Meghdadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Microbiology, Faculty 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, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ameneh Alami
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Reza Tabandeh
- Department of Basic Sciences, Division of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Clinical and Pathological Findings Associated with Mycobacteriosis in Captive Syngnathids. Animals (Basel) 2022; 12:ani12233259. [PMID: 36496780 PMCID: PMC9735937 DOI: 10.3390/ani12233259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Mycobacteriosis is an important disease that affects captive and wild aquatic fish. Syngnathids are susceptible to infection by non-tuberculous mycobacteria. The aim of this study was to describe clinical signs, and macroscopic and histological lesions in 25 syngnathids and the molecular characterization of the causative mycobacteria. Clinical presentation ranged from sudden death to non-specific signs, including anorexia, poor body condition, weight loss and marked dyspnea with increased respiratory effort and rate. Gross lesions were mostly ulcers on the tail and small white nodules in the liver, coelomic cavity and inside the eye. The most affected organs were gills, liver, intestine and coelomic mesentery. Microscopic lesions consisted of areas of multifocal to diffuse granulomatous inflammation and bacterial emboli with numerous intralesional acid-fast bacilli. Epithelioid cells, multinucleated giant cells, lymphocytes and fibrous connective tissue, which are commonly observed in granulomatous inflammation, were not observed here. In the real-time PCR, M. fortuitum, M. chelonae and M. marinum common primers, Mycobacterium spp. were detected in 4, 7 and 14 individuals, respectively. In addition, this is the first description of mycobacteriosis found in Syngnathus acus.
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Khosravi AD, Hashemzadeh M, Rokhfirooz P. Molecular identification of nontuberculous mycobacteria using the rpoB, argH and cya genes analysis. AMB Express 2022; 12:121. [PMID: 36121509 PMCID: PMC9483868 DOI: 10.1186/s13568-022-01463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Nontuberculous mycobacterial (NTM) infections are growing worldwide especially in immunocompromised individuals. Since treatment of NTM infections is species-specific, the precise identification of NTM to species level is critical for an optimal treatment. This study was aimed to identify different NTM species by sequencing the rpoB gene and evaluating the effectiveness of argH and cya gene markers. In total 64 clinical isolates suspected to NTM were collected. The identification of the isolates was done by standard conventional methods and PCR-based rpoB gene and sequence analysis. PCR sequencing of argH and cya genes was performed to evaluate the efficacy of these genes in identifying and differentiating different species and subspecies of NTM. Among 64 isolates tested, 51 (79.68%) were detected by conventional tests as NTM. The results of rpoB sequence analysis revealed that the 56 clinical isolates were identified in 10 species of NTM and 8 remaining isolates which showed ambiguous results by rpoB sequencing, application of argH and cya sequencing could detect these isolates. Furthermore, by using cya gene sequencing, M. abscessus subspecies were properly differentiated. Although the rpoB sequencing as a standard method, is beneficial for detecting various species of NTM, however, based on our findings, argH and cya gene markers have a superb ability to discriminate closely related species. Further investigations are required to verify our outcomes.
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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, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Iranian Group On Microbial Drug Resistance, Tehran, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parisa Rokhfirooz
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Pargami HN, Siadat SD, Amiri V, Sheikhpour M. Antibiotic delivery evaluation against Mycobacterium fortuitum using nanofluids containing carbon nanotubes. BMC Microbiol 2022; 22:96. [PMID: 35410123 PMCID: PMC8996581 DOI: 10.1186/s12866-022-02523-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Background Mycobacterium fortuitum (M. fortuitum) is a bacterium, which can cause infections in many anatomical regions of the body, including the skin, lymph nodes, and joints. This bacterium, which belongs to a group of bacteria known as nontuberculous mycobacteria, is regarded as an important nosocomial pathogen worldwide owing to its increasing antibiotic resistance. Recently, the antimicrobial effects of carbon nanotubes have been reported in numerous studies. These nanotubes can be very useful in drug delivery; besides, they exhibit unique properties against multidrug-resistant bacterial infections. This study aimed to investigate the antimicrobial effects of carboxyl-functionalized multi-walled carbon nanotubes (MWCNT-COOH) to reduce antibiotic resistance. Methods In this study, antibacterial effects of nanofluids containing functionalized MWCNTs at initial concentration of 2 mg/mL and serial dilutions of 54, 28.5, 14.25, 7.12, 3.5 µg/mL, antibiotics alone and combination of nanofluids with antibiotics were investigated. Standard and resistant strains of M. fortuitum were obtained from the microbial bank of the Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran. Results It was observed that nanofluid containing MWCNT-COOH can exert antimicrobial effects on M. fortuitum and significantly reduce bacterial resistance to antibiotics including kanamycin and streptomycin. In the presence of antibiotics and nanofluids containing MWCNT-COOH at a dose of 28.5 µg/mL, no growth was observed. Conclusion One of the main antimicrobial mechanisms of MWCNT-COOH is penetration into the bacterial cell wall. In this study, by using the nanofluid containing MWCNT-COOH with increased stability, the antibiotic resistance of M. fortuitum was significantly reduced at lower dilutions compared to the antibiotic alone. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02523-z.
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Affiliation(s)
- Hamid Naderi Pargami
- Department of Biology, Faculty of Life Sciences, Danesh Alborz University, Abyek, Iran.,Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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5
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Rapid identification of Mycobacterium species isolated from clinical specimens of city Jahrom by real time PCR. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chin KL, Sarmiento ME, Mustapha ZA, Jani J, Jamal NB, Stanis CS, Acosta A. Identification of a Mycobacterium tuberculosis-specific gene marker for diagnosis of tuberculosis using semi-nested melt-MAMA qPCR (lprM-MAMA). Tuberculosis (Edinb) 2020; 125:102003. [PMID: 33099253 DOI: 10.1016/j.tube.2020.102003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is the deadliest of infectious diseases. TB diagnosis, based on sputum microscopy, culture, and nucleic acid amplification tests (NAATs) to identify its main causative agent, Mycobacterium tuberculosis (MTB), remains challenging. The current available NAATs, endorsed by World Health Organization (WHO), can differentiate MTB from some MTB complex (MTBC) members. Using bioinformatics, we identified a single nucleotide polymorphism (SNP) in lprM (Rv1970) gene that differentiate MTB from other MTBC members. A forward mismatch amplification mutation assay (MAMA) primer was designed for the targeted mutation and was used in a semi-nested melt-MAMA qPCR (lprM-MAMA). Using the optimized protocol, lprM-MAMA was positive with all MTB reference and clinical strains, and negative with other MTBC members, non-tuberculous mycobacteria (NTM) and other non-mycobacterial (NM) reference strains. The limit of detection (LOD) of lprM-MAMA was 76.29 fg. Xpert® MTB/RIF (Xpert)-positive sputum samples were also positive by lprM-MAMA, except for samples classified as having "very low" bacterial load by Xpert. Xpert-negative sputum samples were also negative by lprM-MAMA. In conclusion, lprM-MAMA demonstrated to be a useful tool for specific MTB diagnosis. Further evaluation with higher number of reference strains, including NTM and NM; and sputum samples are required to determine its potential for clinical application.
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Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Zainal Arifin Mustapha
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Jaeyres Jani
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Norfazirah Binti Jamal
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Cheronie Shely Stanis
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
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Grandjean Lapierre S, Drancourt M. rpoB Targeted Loop-Mediated Isothermal Amplification (LAMP) Assay for Consensus Detection of Mycobacteria Associated With Pulmonary Infections. Front Med (Lausanne) 2018; 5:332. [PMID: 30547031 PMCID: PMC6279915 DOI: 10.3389/fmed.2018.00332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid method which has been used to identify mycobacteria including Mycobacterium tuberculosis in clinical microbiology laboratory and point of care settings. Previously published LAMP protocols for detection of mycobacterial species used conventional specific primer and targeted the 16S rRNA, gyrB, and insertion sequence genes. We developed and evaluated a LAMP assay targeting a mycobacterial rpoB gene conserved sequence and incorporating degenerate primers. This assay allowed consensus detection of mycobacterial species from pure culture, clinical respiratory tract samples, and mycobacteria growth indicator tube (MGIT) liquid-based culture medium. A panel of twenty mycobacterial species were successfully detected at detection thresholds of 102 CFU/mL and 103 CFU/mL when respectively performed on pure culture suspension or sputum and MGIT broth. The inclusion of degenerate bases in LAMP primers increased the diversity of mycobacterial species identified by the assay without negatively affecting analytical sensitivity. LAMP-based consensus detection of multiple pathogens can be achieved with degenerate primers therefore allowing the design of rapid multi-disease screening assays. Despite high analytical sensitivity, species specificity and the advantageous operational characteristics of LAMP over PCR, challenges such as potential ambiguity in visual interpretation of results and occasional non-specific amplification precludes the implementation of novel LAMP assay in routine diagnostics both in centralized and point-of-care laboratory.
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Affiliation(s)
- Simon Grandjean Lapierre
- Aix-Marseille Université, IRD 198, MEPHI, IHU Méditerranée Infection, Marseille, France
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Michel Drancourt
- Aix-Marseille Université, IRD 198, MEPHI, IHU Méditerranée Infection, Marseille, France
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Mohammadi S, Esfahani BN, Moghim S, Mirhendi H, Zaniani FR, Safaei HG, Fazeli H, Salehi M. Optimal DNA Isolation Method for Detection of Nontuberculous Mycobacteria by Polymerase Chain Reaction. Adv Biomed Res 2017; 6:133. [PMID: 29279831 PMCID: PMC5674650 DOI: 10.4103/2277-9175.217216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a group of opportunistic pathogens and these are widely dispersed in water and soil resources. Identification of mycobacteria isolates by conventional methods including biochemical tests, growth rates, colony pigmentation, and presence of acid-fast bacilli is widely used, but these methods are time-consuming, labor-intensive, and may sometimes remain inconclusive. Materials and Methods The DNA was extracted from NTM cultures using CTAB, Chelex, Chelex + Nonidet P-40, FTA® Elute card, and boiling The quantity and quality of the DNA extracted via these methods were determined using UV-photometer at 260 and 280 nm, and polymerase chain reaction (PCR) amplification of the heat-shock protein 65 gene with serially diluted DNA samples. Results The CTAB method showed more positive results at 1:10-1:100,000 at which the DNA amount was substantial. With the Chelex method of DNA extraction, PCR amplification was detected at 1:10 and 1:1000 dilutions. Conclusions According to the electrophoresis results, the CTAB and Chelex DNA extraction methods were more successful in comparison with the others as regard producing suitable concentrations of DNA with the minimum use of PCR inhibitor.
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Affiliation(s)
- Samira Mohammadi
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Riyahi Zaniani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hajieh Ghasemian Safaei
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Fazeli
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahshid Salehi
- Regional Tuberculosis Reference Laboratories in Isfahan, Isfahan, Iran
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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] [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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Detection of embB Gene Mutations in EMB-Resistant Mycobacterium tuberculosis Isolates From Isfahan Province by PCR-SSCP and Direct Sequencing. Jundishapur J Microbiol 2016. [DOI: 10.5812/jjm.39594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Nasr Esfahani B, Zarkesh Esfahani FS, Bahador N, Moghim S, Radaei T, Rezaei Yazdi H, Ghasemian Safaei H, Fazeli H. Analysis of DNA gyrA Gene Mutation in Clinical and Environmental Ciprofloxacin-Resistant Isolates of Non-Tuberculous Mycobacteria Using Molecular Methods. Jundishapur J Microbiol 2016; 9:e30018. [PMID: 27217921 PMCID: PMC4870840 DOI: 10.5812/jjm.30018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/20/2015] [Accepted: 12/22/2015] [Indexed: 12/20/2022] Open
Abstract
Background During the past several years, nontuberculous mycobacteria (NTM) have been reported as some of the most important agents of infection in immunocompromised patients. Objectives The aim of this study was to evaluate the ciprofloxacin susceptibility of clinical and environmental NTM species isolated from Isfahan province, Iran, using the agar dilution method, and to perform an analysis of gyrA gene-related ciprofloxacin resistance. Materials and Methods A total of 41 clinical and environmental isolates of NTM were identified by conventional and multiplex PCR techniques. The isolates were separated out of water, blood, abscess, and bronchial samples. The susceptibility of the isolates to 1 µg/mL, 2 µg/mL and 4 µg/mL of ciprofloxacin concentrations was determined by the agar dilution method according to CLSI guidelines. A 120-bp area of the gyrA gene was amplified, and PCR-SSCP templates were defined using polyacrylamide gel electrophoresis. The 120-bp of gyrA amplicons with different PCR-SSCP patterns were sequenced. Results The frequency of the identified isolates was as follows: Mycobacterium fortuitum, 27 cases; M. gordonae, 10 cases; M. smegmatis, one case; M. conceptionense, one case; and M. abscessus, two cases. All isolates except for M. abscessus were sensitive to all three concentrations of ciprofloxacin. The PCR-SSCP pattern of the gyrA gene of resistant M. abscessus isolates showed four different bands. The gyrA sequencing of resistant M. abscessus isolates showed 12 alterations in nucleotides compared to the M. abscessus ATCC 19977 resistant strain; however, the amino acid sequences were similar. Conclusions This study demonstrated the specificity and sensitivity of the PCR-SSCP method for finding mutations in the gyrA gene. Due to the sensitivity of most isolates to ciprofloxacin, this antibiotic should be considered an appropriate drug for the treatment of related diseases.
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Affiliation(s)
- Bahram Nasr Esfahani
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Fatemeh Sadat Zarkesh Esfahani
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran
- Corresponding author: Fatemeh Sadat Zarkesh Esfahani, Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran. Tel: +98-9133007218, Fax: +98-3133932376, E-mail:
| | - Nima Bahador
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran
| | - Sharareh Moghim
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Tooba Radaei
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hadi Rezaei Yazdi
- Department of Microbiology, Jahrom University of Medical Sciences, Jahrom, IR Iran
| | | | - Hossein Fazeli
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
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Hadifar S, Moghim S, Fazeli H, GhasemianSafaei H, Havaei SA, Farid F, Esfahani BN. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene. Adv Biomed Res 2015; 4:152. [PMID: 26380237 PMCID: PMC4550954 DOI: 10.4103/2277-9175.161579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 02/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species.
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Affiliation(s)
- Shima Hadifar
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hajieh GhasemianSafaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Fariba Farid
- Department of Health, Isfahan Provincial Health Office, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
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13
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Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
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Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Bainomugisa A, Wampande E, Muchwa C, Akol J, Mubiri P, Ssenyungule H, Matovu E, Ogwang S, Joloba M. Use of real time polymerase chain reaction for detection of M. tuberculosis, M. avium and M. kansasii from clinical specimens. BMC Infect Dis 2015; 15:181. [PMID: 25884439 PMCID: PMC4424587 DOI: 10.1186/s12879-015-0921-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 04/01/2015] [Indexed: 12/25/2022] Open
Abstract
Background The incidence of M. tuberculosis (MTB) and non tuberculous Mycobacterium species (NTMs) like M. avium and M. kansasii has increased due to Human Immunodeficiency Virus (HIV) epidemic. Therefore accurate, rapid and cost effective methods for the identification of these NTMs and MTB are greatly needed for appropriate TB management. Thus in this study we evaluated the performance of Lightcycler® Mycobacterium detection assay to detect MTB, M. avium and M. kansasii in sputum specimens. Methods A total of 241 baseline minimally processed sputum specimens from individual adult TB suspected patients were analyzed by Mycobacterium detection assay (Real-time-PCR) on a LightCycler 480® while using liquid culture as a reference standard. Results Real time PCR had a sensitivity of 100% (95% CI 96–100) and 100% (CI 19–100) for detection of MTB and M. avium respectively. Additionally the assay had a specificity of 99% (95% CI 96–99) and 95% (95% CI 91–97) for identification of MTB and M. avium respectively. The positive predictive value (PPV) for Real time PCR to identify MTB and M. avium among the specimens was 98% (95% CI 94–99) and 15% (95% CI 2–45) respectively. The kappa statistics for Real time PCR to identify MTB and M. avium was 0.9 (95% CI 0.9–1.0) and 0.3 (95% CI–0.03–0.5) respectively. The median time to detection for Real time PCR assay was 2 hours while overall median time to detection for MGIT-positive cultures was 8 days. The sample unit cost for Real time PCR was $ 12 compared to $ 20 for the reference liquid culture. Conclusion The Light cycler® Mycobacterium detection assay rapidly and correctly identified MTB and M avium thus has the potential to be adopted in a clinical setting.
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Affiliation(s)
- Arnold Bainomugisa
- Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Eddie Wampande
- Department of Medical Microbiology, College of Health sciences, Makerere University, Kampala, Uganda. .,Department of Bio molecular Resources and Bio laboratory Sciences, College of Veterinary Medicine, Animal resource and Bio-security, Kampala, Uganda.
| | - Chris Muchwa
- Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Joseph Akol
- Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Paul Mubiri
- Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Henry Ssenyungule
- Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Enock Matovu
- Department of Bio molecular Resources and Bio laboratory Sciences, College of Veterinary Medicine, Animal resource and Bio-security, Kampala, Uganda.
| | - Sam Ogwang
- Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
| | - Moses Joloba
- Department of Medical Microbiology, College of Health sciences, Makerere University, Kampala, Uganda. .,Uganda-CASE Research Collaboration, Kampala, Uganda.
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15
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Detection of mycobacteria, Mycobacterium avium subspecies, and Mycobacterium tuberculosis complex by a novel tetraplex real-time PCR assay. J Clin Microbiol 2015; 53:930-40. [PMID: 25588660 DOI: 10.1128/jcm.03168-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis complex, Mycobacterium avium, and many other nontuberculous mycobacteria are worldwide distributed microorganisms of major medical and veterinary importance. Considering the growing epidemiologic significance of wildlife-livestock-human interrelation, developing rapid detection tools of high specificity and sensitivity is vital to assess their presence and accelerate the process of diagnosing mycobacteriosis. Here we describe the development and evaluation of a novel tetraplex real-time PCR for simultaneous detection of Mycobacterium genus, M. avium subspecies, and M. tuberculosis complex in an internally monitored single assay. The method was evaluated using DNA from mycobacterial (n = 38) and nonmycobacterial (n = 28) strains, tissues spiked with different CFU amounts of three mycobacterial species (n = 57), archival clinical samples (n = 233), and strains isolated from various hosts (n = 147). The minimum detectable DNA amount per reaction was 50 fg for M. bovis BCG and M. kansasii and 5 fg for M. avium subsp. hominissuis. When spiked samples were analyzed, the method consistently detected as few as 100 to 1,000 mycobacterial CFU per gram. The sensitivity and specificity values for the panel of clinical samples were 97.5 and 100% using a verified culture-based method as the reference method. The assays performed on clinical isolates confirmed these results. This PCR was able to identify M. avium and M. tuberculosis complex in the same sample in one reaction. In conclusion, the tetraplex real-time PCR we designed represents a highly specific and sensitive tool for the detection and identification of mycobacteria in routine laboratory diagnosis with potential additional uses.
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Tran AC, Halse TA, Escuyer VE, Musser KA. Detection of Mycobacterium avium complex DNA directly in clinical respiratory specimens: opportunities for improved turn-around time and cost savings. Diagn Microbiol Infect Dis 2014; 79:43-8. [DOI: 10.1016/j.diagmicrobio.2014.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/15/2023]
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Yin X, Zheng L, Lin L, Hu Y, Zheng F, Hu Y, Wang Q. Commercial MPT64-based tests for rapid identification of Mycobacterium tuberculosis complex: A meta-analysis. J Infect 2013; 67:369-77. [DOI: 10.1016/j.jinf.2013.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/04/2013] [Accepted: 06/15/2013] [Indexed: 11/26/2022]
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Yin X, Zheng L, Wu L, Cao N, Zheng F, Hu Y, Lin M, Zhang P, Wang Q. Comparative evaluation of two rapid methods for differentiating mycobacteria. Tuberculosis (Edinb) 2013; 93:227-31. [PMID: 23414675 DOI: 10.1016/j.tube.2013.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
The real-time PCR with duplex primer sets and the MPB64-based immunochromatographic assay are newly developed methods for rapid differentiation of mycobacteria. The aim of this study is to evaluate the two methods for differentiation between Mycobacterium tuberculosis complex and nontuberculous mycobacteria. A total of 95 clinical mycobacterial isolates belonging to 22 different species and 16 reference strains of 16 different species were differentiated by duplex real-time PCR method and MPB64-based immunochromatographic assay method. The two methods were evaluated by comparison with conventional biochemical technique as the gold standard method. The duplex real-time PCR method correctly differentiated all reference strains as well as the MPB64-based immunochromatographic assay method. For clinical isolates, the accuracy of the duplex real-time PCR method (100%) was slightly higher than the MPB64-based immunochromatographic assay method (97.9%), but there was no statistical significance between the two methods (P > 0.05), and there was an excellent agreement between them (Kappa = 0.957). The duplex real-time PCR method possesses greater potential for differentiation of mycobacteria in the clinical laboratory than the MPB64-based immunochromatographic assay method. However, the MPB64-based immunochromatographic assay method is more convenient than the duplex real-time PCR method when the number of sample is small.
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Affiliation(s)
- Xiaomao Yin
- Laboratory Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
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