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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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2
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Abstract
Nontuberculous mycobacteria (NTM) are important pathogens, with a longitudinal prevalence of up to 20% within the cystic fibrosis (CF) population. Diagnosis of NTM pulmonary disease in people with CF (pwCF) is challenging, as a majority have NTM infection that is transient or indolent, without evidence of clinical consequence. In addition, the radiographic and clinical manifestations of chronic coinfections with typical CF pathogens can overlap those of NTM, making diagnosis difficult. Comprehensive care of pwCF must be optimized to assess the true clinical impact of NTM and to improve response to treatment. Treatment requires prolonged, multidrug therapy that varies depending on NTM species, resistance pattern, and extent of disease. With a widespread use of highly effective modulator therapy (HEMT), clinical signs and symptoms of NTM disease may be less apparent, and sensitivity of sputum cultures further reduced. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in pwCF is a research priority, as a lifelong strategy is needed for this high-risk population.
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3
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The first diagnostic test for specific detection of Mycobacterium simiae using an electrochemical label-free DNA nanobiosensor. Talanta 2022; 238:123049. [PMID: 34801906 DOI: 10.1016/j.talanta.2021.123049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/06/2021] [Accepted: 11/06/2021] [Indexed: 01/08/2023]
Abstract
Mycobacterium simiae has been reported to be the most prevalent species of Nontuberculous mycobacteria (NTM) in many countries. As both phenotypic and molecular detection of M. simiae and other NTMs have limitations, finding an accurate, fast, and low-cost diagnostic method is critical for the management of infections. Here, we report the development of a new type of label-free electrochemical biosensor using a gold electrode decorated with l-cysteine/PAMAM dendrimer for specific targeting of M. simiae ITS sequence. DNA hybridization was monitored by measuring changes in the free guanine electrical signal with changing ssDNA target concentrations by differential pulse voltammetry (DPV) method. Response surface methodology (RSM) was applied for the optimization of variables affecting biosensor response. Under optimal conditions, the biosensor revealed a wide linear range from 10-14 M to 10-6 M and a detection limit of 1.40 fM. The fabricated biosensor showed an excellent selectivity to M. simiae in the presence of other similar pathogenic bacteria. Moreover, experimental results confirmed that this biosensor exhibited great precision and high reproducibility, hence provides a low-cost, label-free, and faster detection analysis, representing a novel strategy in detecting other NTMs.
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High rate of reinfection and possible transmission of Mycobacterium avium complex in Northeast Thailand. One Health 2022; 14:100374. [PMID: 35198722 PMCID: PMC8855214 DOI: 10.1016/j.onehlt.2022.100374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/12/2021] [Accepted: 02/06/2022] [Indexed: 11/20/2022] Open
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5
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Lekko YM, Ooi PT, Omar S, Mazlan M, Ramanoon SZ, Jasni S, Jesse FFA, Che-Amat A. Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis. Vet World 2020; 13:1822-1836. [PMID: 33132593 PMCID: PMC7566238 DOI: 10.14202/vetworld.2020.1822-1836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, which affects various domestic animals, wildlife, and humans. Some wild animals serve as reservoir hosts in the transmission and epidemiology of the disease. Therefore, the monitoring and surveillance of both wild and domestic hosts are critical for prevention and control strategies. For TB diagnosis, the single intradermal tuberculin test or the single comparative intradermal tuberculin test, and the gamma-interferon test, which is regarded as an ancillary test, are used. Postmortem examination can identify granulomatous lesions compatible with a diagnosis of TB. In contrast, smears of the lesions can be stained for acid-fast bacilli, and samples of the affected organs can be subjected to histopathological analyses. Culture is the gold standard test for isolating mycobacterial bacilli because it has high sensitivity and specificity compared with other methods. Serology for antibody detection allows the testing of many samples simply, rapidly, and inexpensively, and the protocol can be standardized in different laboratories. Molecular biological analyses are also applicable to trace the epidemiology of the disease. In conclusion, reviewing the various techniques used in MTBC diagnosis can help establish guidelines for researchers when choosing a particular diagnostic method depending on the situation at hand, be it disease outbreaks in wildlife or for epidemiological studies. This is because a good understanding of various diagnostic techniques will aid in monitoring and managing emerging pandemic threats of infectious diseases from wildlife and also preventing the potential spread of zoonotic TB to livestock and humans. This review aimed to provide up-to-date information on different techniques used for diagnosing TB at the interfaces between wildlife, livestock, and humans.
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Affiliation(s)
- Yusuf Madaki Lekko
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Maiduguri, 1069 PMB, Maiduguri, Borno State, Nigeria
| | - Peck Toung Ooi
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sharina Omar
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mazlina Mazlan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Zubaidah Ramanoon
- Department of Farm and Exotic Animal Medicine and Surgery, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sabri Jasni
- Department of Paraclinical, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Faez Firdaus Abdullah Jesse
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Azlan Che-Amat
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Singh K, Kumari R, Tripathi R, Gupta S, Anupurba S. Detection of clinically important non tuberculous mycobacteria (NTM) from pulmonary samples through one-step multiplex PCR assay. BMC Microbiol 2020; 20:267. [PMID: 32847517 PMCID: PMC7448335 DOI: 10.1186/s12866-020-01952-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 11/10/2022] Open
Abstract
Background The burden of non-tuberculous mycobacterial (NTM) disease is increasing worldwide but still its diagnosis is delayed and it is mistaken as multidrug-resistant tuberculosis (MDR-TB).The present study was performed to develop a multiplex PCR assay for detection and identification of clinically most common NTM to the species level from pulmonary samples. Results Out of 50 isolates, 26 were identified as Mycobacterium kansasii (MK), 20 were identified as Mycobacterium abscessus (MA) and 4 were identified as Mycobacterium avium complex (MAC) through multiplex PCR and further confirmed by sequencing. Conclusion Our study showed that multiplex PCR assay is a simple, convenient, and reliable technique for detection and differential identification of major NTM species.
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Affiliation(s)
- Kamal Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Richa Kumari
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rajneesh Tripathi
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Smita Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
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7
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Simon A, Onya O, Mazza-Stalder J, Nicod L, Gilbert G, Katia J. Added diagnostic value of 16S rRNA gene pan-mycobacterial PCR for nontuberculous mycobacterial infections: a 10-year retrospective study. Eur J Clin Microbiol Infect Dis 2019; 38:1873-1881. [PMID: 31313101 PMCID: PMC6778528 DOI: 10.1007/s10096-019-03621-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/15/2022]
Abstract
The diagnosis of mycobacterial infections has been dramatically improved by the introduction of molecular methods aimed to reduce the time to diagnosis as compared with culture. The broad range pan-mycobacterial PCR can detect all the mycobacterial species directly from clinical specimens. We aimed to evaluate its usefulness and its clinical added value for the diagnosis of nontuberculous mycobacterial (NTM) infections. We performed a retrospective study (2003-2013) including 952 samples taken from 639 patients with clinical suspicion of NTM infection. The performance of smear microscopy, PCR and culture was established using clinical data to investigate discrepant results. We also compared the time to microbial diagnosis between the direct PCR and culture. The sensitivity, specificity, positive and negative predictive values of the PCR were 61.6% (53.5-69.1), 99.1% (98.2-99.6), 92.8% (85.8-96.5) and 93.4% (91.6-94.9), respectively, when considering all specimens. When considering smear-positive specimens and smear-negative specimens, the sensitivity was 81.6% and 40%, respectively. The sensitivity for pulmonary and extra-pulmonary smear-positive specimens was 85.2% versus 72.7%. The median time to identification at species level was 35 days (SD, 17.67) for culture and 6 days (SD, 2.67) for the PCR (when positive), which represents a 29-day shorter time to results (p < 0.0001). The 16S rRNA gene pan-mycobacterial PCR displays a substantial benefit in terms of time to diagnose NTM infections when compared with culture. Despite an excellent specificity, its sensitivity is yet limited in particular for smear-negative specimens, which might be improved by relying onto real-time PCRs.
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Affiliation(s)
- Andenmatten Simon
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Opota Onya
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland.
| | - Jesica Mazza-Stalder
- Division of Pulmonology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Laurent Nicod
- Division of Pulmonology, University of Lausanne and University Hospital of Lausanne, Lausanne, Switzerland
| | - Greub Gilbert
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Jaton Katia
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland.
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Dowdell K, Haig SJ, Caverly LJ, Shen Y, LiPuma JJ, Raskin L. Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation. Curr Opin Biotechnol 2019; 57:127-136. [PMID: 31003169 DOI: 10.1016/j.copbio.2019.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/18/2022]
Abstract
Nontuberculous mycobacteria (NTM) pulmonary infections are a growing concern worldwide, with a disproportionate incidence in persons with pre-existing health conditions. NTM have frequently been found in municipally-treated drinking water and building plumbing, leading to the hypothesis that an important source of NTM exposure is drinking water. The identification and quantification of NTM in environmental samples are complicated by genetic variability among NTM species, making it challenging to determine if clinically relevant NTM are present. Additionally, their unique cellular features and lifestyles make NTM and their nucleic acids difficult to recover. This review highlights a recent work focused on quantification and characterization of NTM and on understanding the influence of source water, treatment plants, distribution systems, and building plumbing on the abundance of NTM in drinking water.
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Affiliation(s)
- Katherine Dowdell
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Yun Shen
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA.
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Abstract
Nontuberculous mycobacteria (NTM) are important emerging cystic fibrosis (CF) pathogens, with estimates of prevalence ranging from 6% to 13%. Diagnosis of NTM disease in patients with CF is challenging, as the infection may remain indolent in some, without evidence of clinical consequence, whereas other patients suffer significant morbidity and mortality. Treatment requires prolonged periods of multiple drugs and varies depending on NTM species, resistance pattern, and extent of disease. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in CF patients is a research priority, as a lifelong strategy is needed for this high-risk population.
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Affiliation(s)
- Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Denver School of Medicine, 13123 East 16th Avenue, Box B-395, Aurora, CO 80045, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA.
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Jung MJ, Chung BY, Choi YW, Son JH, Kim HO, Park CW. A Case of Cutaneous Non-Mycobacterium Infection after Illegal Botulinum Toxin Injection Diagnosed by Polymerase Chain Reaction. Ann Dermatol 2019; 31:242-244. [PMID: 33911582 PMCID: PMC7992686 DOI: 10.5021/ad.2019.31.2.242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 11/20/2022] Open
Affiliation(s)
- Min Je Jung
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Bo Young Chung
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Yong Won Choi
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Jee Hee Son
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Hye One Kim
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Chun Wook Park
- Department of Dermatology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
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11
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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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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16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria. PLoS One 2016; 11:e0164138. [PMID: 27749897 PMCID: PMC5066948 DOI: 10.1371/journal.pone.0164138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/20/2016] [Indexed: 11/29/2022] Open
Abstract
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included. Identification was compared with that achieved by high performance liquid chromatography (HPLC), in-house PCR and 16S/ITS sequencing. Isolates of all species yielded a SCGE profile comprising a single fragment length (or peak) except for M. scrofulaceum (two peaks). SCGE peaks of ATCC strains were distinct except for peak overlap between Mycobacterium kansasii and M. marinum. Of clinical/environmental strains, unique peaks were seen for 7/17 (41%) species (M. haemophilum, M. kubicae, M. lentiflavum, M. terrae, M. kansasii, M. asiaticum and M. triplex); 3/17 (18%) species were identified by HPLC. There were five SCGE fragment length types (I–V) each of M. avium, M. intracellulare and M. gordonae. Overlap of fragment lengths was seen between M. marinum and M. ulcerans; for M. gordonae SCGE type III and M. paragordonae; M. avium SCGE types III and IV, and M. intracellulare SCGE type I; M. chimaera, M. parascrofulaceum and M. intracellulare SCGE types III and IV; M. branderi and M. avium type V; and M. vulneris and M. intracellulare type V. The ITS-SCGE method was able to provide the first line rapid and reproducible species identification/screening of SG-NTM and was more discriminatory than HPLC.
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Mycobacterium abscessus. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2016. [DOI: 10.1097/ipc.0000000000000385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Culture-Independent Detection of Nontuberculous Mycobacteria in Clinical Respiratory Samples. J Clin Microbiol 2016; 54:2395-8. [PMID: 27413194 DOI: 10.1128/jcm.01410-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/20/2022] Open
Abstract
Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory samples is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical samples that is specific, sensitive, and robust.
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Martiniano SL, Nick JA, Daley CL. Nontuberculous Mycobacterial Infections in Cystic Fibrosis. Clin Chest Med 2015; 37:83-96. [PMID: 26857770 DOI: 10.1016/j.ccm.2015.11.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nontuberculous mycobacteria (NTM) are important emerging cystic fibrosis (CF) pathogens, with estimates of prevalence ranging from 6% to 13%. Diagnosis of NTM disease in patients with CF is challenging, as the infection may remain indolent in some, without evidence of clinical consequence, whereas other patients suffer significant morbidity and mortality. Treatment requires prolonged periods of multiple drugs and varies depending on NTM species, resistance pattern, and extent of disease. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in CF patients is a research priority, as a lifelong strategy is needed for this high-risk population.
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Affiliation(s)
- Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Denver School of Medicine, 13123 East 16th Avenue, Box B-395, Aurora, CO 80045, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA.
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Martiniano SL, Nick JA. Nontuberculous Mycobacterial Infections in Cystic Fibrosis. Clin Chest Med 2015; 36:101-15. [DOI: 10.1016/j.ccm.2014.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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A Novel Mycobacterium cosmeticum-Like Bacterium Isolated from the Ear Swab of a Patient with Otitis Externa. Case Rep Infect Dis 2015; 2015:825819. [PMID: 25866687 PMCID: PMC4381726 DOI: 10.1155/2015/825819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/10/2015] [Indexed: 11/28/2022] Open
Abstract
We describe the identification and characterization of a novel nontuberculous mycobacterium (NTM), isolated from an ear swab of an adult male patient with chronic otitis externa. Genetically, the bacterium is most closely related to Mycobacterium cosmeticum; however, growth and biochemical features indicate that it is distinctly different. Here, we highlight for the first time an unusual NTM that is a probable cause of ear infection.
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Ferrand J, Patron K, Legrand-Frossi C, Frippiat JP, Merlin C, Alauzet C, Lozniewski A. Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice. J Microbiol Methods 2014; 105:180-5. [PMID: 25093756 DOI: 10.1016/j.mimet.2014.07.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/25/2014] [Accepted: 07/25/2014] [Indexed: 01/22/2023]
Abstract
Analysis of bacterial DNA from fecal samples of mice is commonly performed in experimental studies. Although DNA extraction is a critical step in various molecular approaches, the efficiency of methods that may be used for DNA extraction from mice fecal samples has never been evaluated. We compared the efficiencies of six widely used commercial kits (MasterPure™ Gram Positive DNA Purification Kit, QIAamp® DNA Stool Mini Kit; NucliSENS® easyMAG®, ZR Fecal DNA MiniPrep™, FastDNA® SPIN Kit for Feces and FastDNA® SPIN Kit for Soil) and a non-commercial method for DNA isolation from mice feces and cecal contents. DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR. Cell lysis efficiencies were evaluated by qPCR targeting three relevant bacteria in spiked specimens. For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.
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Affiliation(s)
- Janina Ferrand
- EA 7300 Stress Immunité Pathogènes, Université de Lorraine, Vandoeuvre-lès-Nancy, France.
| | - Kevin Patron
- EA 7300 Stress Immunité Pathogènes, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | - Jean-Pol Frippiat
- EA 7300 Stress Immunité Pathogènes, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Christophe Merlin
- Université de Lorraine-CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), UMR, 7564 Vandœuvre-lès-Nancy, France
| | - Corentine Alauzet
- EA 7300 Stress Immunité Pathogènes, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Alain Lozniewski
- EA 7300 Stress Immunité Pathogènes, Université de Lorraine, Vandoeuvre-lès-Nancy, France
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Affiliation(s)
- Ruth C. Lamb
- Alan Lyell Centre for Dermatology; Southern General Hospital; Glasgow UK
| | - Goutam Dawn
- Department of Dermatology; Monklands Hospital; Airdrie UK
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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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Ho J, Balm M, Huggan P, Chew N, Venkatachalam I, Archuleta S. Immune reconstitution inflammatory syndrome associated with disseminated Mycobacterium sherrisii infection. Int J STD AIDS 2012; 23:369-70. [PMID: 22648896 DOI: 10.1258/ijsa.2011.011311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacterium sherrisii is a recently described mycobacterium closely related to Mycobacterium simiae. There have been only a few reports of this organism causing disease, predominantly in the setting of HIV with severe immunosuppression. We report the first case of disseminated M. sherrisii associated with immune reconstitution inflammatory syndrome.
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Affiliation(s)
- J Ho
- Division of Infectious Diseases, National University Hospital Singapore, University Medicine Cluster, 1E Kent Ridge Road, Singapore 119228, Singapore.
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Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria. J Clin Microbiol 2011; 50:483-7. [PMID: 22162553 DOI: 10.1128/jcm.06155-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex real-time PCR assay and melting curve analysis for identifying 23 mycobacterial species was developed and evaluated using 77 reference strains and 369 clinical isolates. Concordant results were obtained for all 189 (100%) isolates of the Mycobacterium tuberculosis complex and 169 (93.9%) isolates of nontuberculous mycobacteria. Our results showed that this multiplex real-time PCR assay is an effective tool for the mycobacterial identification from cultures.
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Camarena Miñana JJ, González Pellicer R. Micobacterias atípicas y su implicación en patología infecciosa pulmonar. Enferm Infecc Microbiol Clin 2011; 29 Suppl 5:66-75. [DOI: 10.1016/s0213-005x(11)70046-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Usefulness of three-channel multiplex real-time PCR and melting curve analysis for simultaneous detection and identification of the Mycobacterium tuberculosis complex and nontuberculous mycobacteria. J Clin Microbiol 2011; 49:3963-6. [PMID: 21918032 DOI: 10.1128/jcm.05662-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We attempted to determine the benefits of three-channel multiplex real-time PCR and melting curve analysis not only in detecting and distinguishing between nontuberculous mycobacteria (NTM) and the Mycobacterium tuberculosis complex but also in identifying NTM to the species level.
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