1
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Hendrikx L, van Hees CLM, de Steenwinkel JEM, Bax HI, Sprong T, Mulder B, Jansz A, van Griethuysen A, Bosboom R, Stemerding A, Koetsier M, van Coevorden M, Mourik BC, Quint KD, Ott A, van Soolingen D, Kuipers S, van Crevel R, van Ingen J. Treatment and Outcome of Culture-Confirmed Mycobacterium marinum Disease. Open Forum Infect Dis 2022; 9:ofac077. [PMID: 35308482 PMCID: PMC8925999 DOI: 10.1093/ofid/ofac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mycobacterium marinum is a nontuberculous mycobacterium that causes skin and soft tissue infections. Treatment consists of multiple antibiotics, sometimes combined with surgical debridement. There is little evidence for the choice of antibiotics, the duration of treatment, and the role of susceptibility testing. Methods We performed a retrospective cohort study of culture-confirmed M. marinum infections in the Netherlands in the 2011–2018 period. Clinical characteristics, in vitro susceptibility, extent of disease, treatment regimens, and outcomes were analyzed. Incidence was assessed from laboratory databases. Results Forty cases of M. marinum infection could be studied. Antibiotic treatment cured 36/40 patients (90%) after a mean treatment duration of 25 weeks. Failure/relapse occurred in 3 patients, and 1 patient was lost to follow-up. Antibiotic treatment consisted of monotherapy in 35% and 2-drug therapy in 63%. Final treatment contained mostly ethambutol–macrolide combinations (35%). Eleven patients (28%) received additional surgery. We recorded high rates of in vitro resistance to tetracyclines (36% of isolates). Tetracycline resistance seemed correlated with poor response to tetracycline monotherapy. The annual incidence rate was 0.15/100 000/year during the study period. Conclusions Prolonged and susceptibility-guided treatment results in a 90% cure rate in M. marinum disease. Two-drug regimens of ethambutol and a macrolide are effective for moderately severe infections. Tetracycline monotherapy in limited disease should be used vigilantly, preferably with proven in vitro susceptibility.
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Affiliation(s)
- Louise Hendrikx
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboudumc Center for Infectious Diseases, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Colette L M van Hees
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jurriaan E M de Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hannelore I Bax
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tom Sprong
- Department of Internal Medicine, Canisius Wilhelmine Hospital, Nijmegen, the Netherlands
| | - Bert Mulder
- Department of Medical Microbiology, Canisius Wilhelmine Hospital, Nijmegen, the Netherlands
| | - Arjan Jansz
- PAMM Laboratory of Medical Microbiology, Veldhoven, the Netherlands
| | | | - Ron Bosboom
- Department of Medical Microbiology, Rijnstate Hospital, Arnhem, the Netherlands
| | - Annette Stemerding
- Department of Medical Microbiology, Gelre Hospital, Apeldoorn, the Netherlands
| | | | | | - Bas C Mourik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Koen D Quint
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alewijn Ott
- Department of Medical Microbiology, Certe, Groningen, the Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Saskia Kuipers
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Reinout van Crevel
- Radboudumc Center for Infectious Diseases, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
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2
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Winthrop KL, Flume PA, Thomson R, Mange KC, Yuen DW, Ciesielska M, Morimoto K, Ruoss SJ, Codecasa LR, Yim JJ, Marras TK, van Ingen J, Wallace RJ Jr, Brown-Elliott BA, Coulter C, Griffith DE. Amikacin Liposome Inhalation Suspension for Mycobacterium avium Complex Lung Disease: A 12-Month Open-Label Extension Clinical Trial. Ann Am Thorac Soc 2021; 18:1147-57. [PMID: 33326356 DOI: 10.1513/AnnalsATS.202008-925OC] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rationale: Patients with refractory Mycobacterium avium complex (MAC) lung disease have limited treatment options. In the CONVERT study, amikacin liposome inhalation suspension (ALIS) added to guideline-based therapy (GBT) increased culture conversion rates versus GBT alone by Month 6. Limited data are available regarding >6-month treatment in a refractory population. Objectives: Evaluate 12-month safety, tolerability, and efficacy of ALIS+GBT. Methods: Adults with refractory MAC lung disease not achieving culture conversion by CONVERT Month 6 could enroll in this open-label extension (INS-312) to receive 590 mg once-daily ALIS+GBT for 12 months. Two cohorts enrolled: the “ALIS-naive” cohort included patients randomized to GBT alone in CONVERT, and the “prior-ALIS” cohort included those randomized to ALIS+GBT in CONVERT. Safety and tolerability of ALIS over 12 months (primary endpoint) and culture conversion by Months 6 and 12 were assessed. Results: In the ALIS-naive cohort, 83.3% of patients (n = 75/90) experienced respiratory treatment-emergent adverse events (TEAEs), and 35.6% (n = 32) had serious TEAEs; 26.7% (n = 24) achieved culture conversion by Month 6 and 33.3% (n = 30) by Month 12. In the prior-ALIS cohort, 46.6% of patients (n = 34/73) experienced respiratory TEAEs, and 27.4% (n = 20) had serious TEAEs; 9.6% (n = 7) achieved culture conversion by Month 6 (≤14 mo ALIS exposure) and 13.7% (n = 10) by Month 12 (≤20 mo ALIS exposure). Nephrotoxicity-related TEAEs and measured hearing decline were infrequent in both cohorts. Conclusions: In up to 20 months of ALIS use, respiratory TEAEs were common, nephrotoxicity and hearing decline were infrequent, and culture conversion continued beyond 6 months of therapy. Clinical trial registered with www.clinicaltrials.gov (NCT02628600).
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3
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Luo L, Cao W, Chen W, Zhang R, Jing L, Chen H, Yu F, Yue J. Evaluation of the VITEK MS knowledge base version 3.0 for the identification of clinically relevant Mycobacterium species. Emerg Microbes Infect 2018; 7:114. [PMID: 29973586 PMCID: PMC6031696 DOI: 10.1038/s41426-018-0120-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 11/09/2022]
Abstract
Different Mycobacterium spp. infections may indicate varied treatment regimens in the clinic. Thus, the species-level identification of Mycobacterium spp. is one of the most important tasks for a clinical microbiology laboratory. Although matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for the identification of mycobacteria, this method lacks a comprehensive evaluation of the identification accuracy for clinically collected mycobacteria using VITEK MS Knowledge Base Version 3.0 (Ver 3.0). The objectives of the present study were to evaluate the identification performance of Mycobacterium spp. using Ver 3.0 and a sample processing kit for strain inactivation and protein extraction. Among the 507 Mycobacterium isolates, 46 isolates were M. tuberculosis, and 461 isolates were nontuberculous mycobacteria (NTM) (including 27 species: 17 species were slowly growing mycobacteria (SGM), and 10 species were rapidly growing mycobacteria (RGM)). The VITEK MS V3.0 library was used to correctly identify 476/507 (93.9%) isolates (425 isolates were correctly identified initially, and 51 more isolates were correctly identified on repeat), 23/507 (4.5%) isolates were unidentified, and 8/507 (1.6%) isolates were misidentified. In summary, we showed that Mycobacterium spp. can be adequately identified by Ver 3.0 in combination with the use of a standard sample processing kit.
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Affiliation(s)
- LiuLin Luo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Wen Cao
- Tongji University School of Medicine, Shanghai, 200092, China
| | - WeiWei Chen
- Tongji University School of Medicine, Shanghai, 200092, China
| | - RanRan Zhang
- Tongji University School of Medicine, Shanghai, 200092, China
| | - LinJie Jing
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - HuiPing Chen
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - FangYou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Jun Yue
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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4
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Nour-Neamatollahie A, Ebrahimzadeh N, Siadat SD, Vaziri F, Eslami M, Akhavan Sepahi A, Khanipour S, Masoumi M, Sakhaee F, Ghazanfari Jajin M, Bahrmand A, Fateh A. Distribution of non-tuberculosis mycobacteria strains from suspected tuberculosis patients by heat shock protein 65 PCR-RFLP. Saudi J Biol Sci 2016; 24:1380-1386. [PMID: 28855835 PMCID: PMC5562452 DOI: 10.1016/j.sjbs.2016.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 12/25/2015] [Revised: 01/24/2016] [Accepted: 02/01/2016] [Indexed: 12/03/2022] Open
Abstract
The genus Mycobacterium contains more than 150 species. Non-tuberculosis mycobacteria (NTM) often cause extrapulmonary and pulmonary disease. Mycobacteria detection at species level is necessary and provides useful information on epidemiology and facilitates successful treatment of patients. This retrospective study aimed to determine the incidence of the NTM isolates and Mycobacterium tuberculosis (Mtb) in clinical specimens collected from Iranian patients during February 2011–December 2013, by PCR–restriction fragment length polymorphism analysis (PRA) of the hsp65 gene. We applied conventional biochemical test and hsp65–PRA identification assay to identify species of mycobacteria in specimens from patients suspected of having mycobacterial isolates. This method was a sensitive, specific and effective assay for detecting mycobacterial species and had a 100% sensitivity and specificity for Mtb and Mycobacterium avium complex (MAC) species. Using PRA for 380 mycobacterial selected isolates, including 317 Mtb, four Mycobacterium bovis and of the 59 clinical isolates, the most commonly identified organism was Mycobacterium kansasii (35.6%), followed by Mycobacterium simiae (16.9%), Mycobacterium gordonae (16.9%), Mycobacterium fortuitum (5.1%), Mycobacterium intracellulare (5.1%), Mycobacterium avium (5.1%), Mycobacterium scrofulaceum (3.4%), Mycobacterium gastri (3.4%), Mycobacterium flavescens (3.4%), Mycobacterium chelonae (3.4%) and Mycobacterium nonchromogenicum (1.7%). PRA method, in comparison with classical methods, is rapid, useful and sensitive for the phylogenetic analysis and species detection of mycobacterial strains. Mycobacterium kansasii is the most common cause of infection by NTM in patients with non-HIV and HIV which demonstrated a high outbreak and diversity of NTM strains in our laboratory.
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Affiliation(s)
- Ali Nour-Neamatollahie
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Department of Microbiology, College of Basic Science, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Eslami
- Young Researchers and Elite Club, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Abbas Akhavan Sepahi
- Department of Microbiology, College of Basic Science, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Sharareh Khanipour
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ahmadreza Bahrmand
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Departments of Mycobacteriology & 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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Tortoli E, Richter E, Borroni E, Cabibbe AM, Capitolo E, Cittaro D, Engel R, Hendricks O, Hillemann D, Kristiansen JE, Mariottini A, Schubert S, Cirillo DM. Mycobacterium alsense sp. nov., a scotochromogenic slow grower isolated from clinical respiratory specimens. Int J Syst Evol Microbiol 2015; 66:450-456. [PMID: 26545358 DOI: 10.1099/ijsem.0.000744] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The name 'Mycobacterium alsiense', although reported in 2007, has not been validly published. Polyphasic characterization of three available strains of this species led us to the conclusion that they represent a distinct species within the genus Mycobacterium. The proposed novel species grows slowly and presents pale yellow-pigmented colonies. Differentiation from other mycobacteria is not feasible on the basis of biochemical and cultural features alone while genetic analysis, extended to eight housekeeping genes and one spacer region, reveals its clear distinction from all other mycobacteria. Mycobacterium asiaticum is the most closely related species on the basis of 16S rRNA gene sequences (similarity 99.3 %); the average nucleotide identity between the genomes of the two species is 80.72 %, clearly below the suggested cut-off (95-96 %). The name Mycobacterium alsense sp. nov. is proposed here for the novel species and replaces the name 'M. alsiense', ex Richter et al. 2007, given at the time of isolation of the first strain. The type strain is TB 1906T ( = DSM 45230T = CCUG 56586T).
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Affiliation(s)
- Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Emanuele Borroni
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea M Cabibbe
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eleonora Capitolo
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Regina Engel
- Structural Biochemistry, Research Center Borstel, Borstel, Germany
| | - Oliver Hendricks
- Department of Physics, Chemistry and Pharmacy, Southern Danish University, Odense, Denmark
| | - Doris Hillemann
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, 138314, Germany
| | | | | | - Sabine Schubert
- Institute for Infection Medicine, University of Kiel and University Medical Center Schleswig-Holstein Campus, Kiel, Germany
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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6
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Ichikawa K, van Ingen J, Koh WJ, Wagner D, Salfinger M, Inagaki T, Uchiya KI, Nakagawa T, Ogawa K, Yamada K, Yagi T. Genetic diversity of clinical Mycobacterium avium subsp. hominissuis and Mycobacterium intracellulare isolates causing pulmonary diseases recovered from different geographical regions. Infect Genet Evol 2015; 36:250-5. [PMID: 26435330 DOI: 10.1016/j.meegid.2015.09.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/09/2015] [Accepted: 09/29/2015] [Indexed: 11/22/2022]
Abstract
Mycobacterium avium complex (MAC) infections are increasing annually in many countries. MAC strains are the most common nontuberculous mycobacterial pathogens isolated from respiratory samples and predominantly consist of two species, Mycobacterium avium and Mycobacterium intracellulare. The aim of this study was to analyze the molecular epidemiology and genetic backgrounds of clinical MAC isolates collected from The Netherlands, Germany, United States, Korea and Japan. Variable numbers of tandem repeats (VNTR) analysis was used to examine the genetic relatedness of clinical isolates of M. avium subsp. hominissuis (n=261) and M. intracellulare (n=116). Minimum spanning tree and unweighted pair group method using arithmetic averages analyses based on the VNTR data indicated that M. avium subsp. hominissuis isolates from Japan shared a high degree of genetic relatedness with Korean isolates, but not with isolates from Europe or the United States, whereas M. intracellulare isolates did not show any specific clustering by geographic origin. The findings from the present study indicate that strains of M. avium subsp. hominissuis, but not M. intracellulare, exhibit geographical differences in genetic diversity and imply that MAC strains may have different sources, routes of transmission and perhaps clinical manifestations.
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7
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Wlodarska M, Johnston JC, Gardy JL, Tang P. A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. Clin Microbiol Rev 2015; 28:523-39. [PMID: 25810419 DOI: 10.1128/CMR.00124-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is an ancient disease with an enormous global impact. Despite declining global incidence, the diagnosis, phenotyping, and epidemiological investigation of TB require significant clinical microbiology laboratory resources. Current methods for the detection and characterization of Mycobacterium tuberculosis consist of a series of laboratory tests varying in speed and performance, each of which yields incremental information about the disease. Since the sequencing of the first M. tuberculosis genome in 1998, genomic tools have aided in the diagnosis, treatment, and control of TB. Here we summarize genomics-based methods that are positioned to be introduced in the modern clinical TB laboratory, and we highlight how recent advances in genomics will improve the detection of antibiotic resistance-conferring mutations and the understanding of M. tuberculosis transmission dynamics and epidemiology. We imagine the future TB clinic as one that relies heavily on genomic interrogation of the M. tuberculosis isolate, allowing for more rapid diagnosis of TB and real-time monitoring of outbreak emergence.
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8
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Abstract
Mycobacteriosis, a chronic bacterial infection, has been associated with severe losses in some zebrafish facilities and low-level mortalities and unknown impacts in others. The occurrence of at least six different described species (Mycobacterium abscessus, M. chelonae, M. fortuitum, M. haemophilum, M. marinum, M. peregrinum) from zebrafish complicates diagnosis and control because each species is unique. As a generalization, mycobacteria are often considered opportunists, but M. haemophilum and M. marinum appear to be more virulent. Background genetics of zebrafish and environmental conditions influence the susceptibility of fish and progression of disease, emphasizing the importance of regular monitoring and good husbandry practices. A combined approach to diagnostics is ultimately the most informative, with histology as a first-level screen, polymerase chain reaction for rapid detection and species identification, and culture for strain differentiation. Occurrence of identical strains of Mycobacterium in both fish and biofilms in zebrafish systems suggests transmission can occur when fish feed on infected tissues or tank detritus containing mycobacteria. Within a facility, good husbandry practices and sentinel programs are essential for minimizing the impacts of mycobacteria. In addition, quarantine and screening of animals coming into a facility is important for eliminating the introduction of the more severe pathogens. Elimination of mycobacteria from an aquatic system is likely not feasible because these species readily establish biofilms on surfaces even in extremely low nutrient conditions. Risks associated with each commonly encountered species need to be identified and informed management plans developed. Basic research on the growth characteristics, disinfection, and pathogenesis of zebrafish mycobacteria is critical moving forward.
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Affiliation(s)
- Christopher M Whipps
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA.
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9
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Pérez-Osorio AC, Boyle DS, Ingham ZK, Ostash A, Gautom RK, Colombel C, Houze Y, Leader BT. Rapid identification of mycobacteria and drug-resistant Mycobacterium tuberculosis by use of a single multiplex PCR and DNA sequencing. J Clin Microbiol 2012; 50:326-36. [PMID: 22162548 DOI: 10.1128/JCM.05570-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) remains a significant global health problem for which rapid diagnosis is critical to both treatment and control. This report describes a multiplex PCR method, the Mycobacterial IDentification and Drug Resistance Screen (MID-DRS) assay, which allows identification of members of the Mycobacterium tuberculosis complex (MTBC) and the simultaneous amplification of targets for sequencing-based drug resistance screening of rifampin-resistant (rifampin(r)), isoniazid(r), and pyrazinamide(r) TB. Additionally, the same multiplex reaction amplifies a specific 16S rRNA gene target for rapid identification of M. avium complex (MAC) and a region of the heat shock protein 65 gene (hsp65) for further DNA sequencing-based confirmation or identification of other mycobacterial species. Comparison of preliminary results generated with MID-DRS versus culture-based methods for a total of 188 bacterial isolates demonstrated MID-DRS sensitivity and specificity as 100% and 96.8% for MTBC identification; 100% and 98.3% for MAC identification; 97.4% and 98.7% for rifampin(r) TB identification; 60.6% and 100% for isoniazid(r) TB identification; and 75.0% and 98.1% for pyrazinamide(r) TB identification. The performance of the MID-DRS was also tested on acid-fast-bacterium (AFB)-positive clinical specimens, resulting in sensitivity and specificity of 100% and 78.6% for detection of MTBC and 100% and 97.8% for detection of MAC. In conclusion, use of the MID-DRS reduces the time necessary for initial identification and drug resistance screening of TB specimens to as little as 2 days. Since all targets needed for completing the assay are included in a single PCR amplification step, assay costs, preparation time, and risks due to user errors are also reduced.
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10
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Kim JU, Cha CH, An HK. Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria. J Clin Microbiol 2012; 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] [What about the content of this article? (0)] [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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11
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Wengenack NL, Hall L. Sequence‐Based Identification and Characterization of Mycobacteria. In: Persing DH, Tenover FC, Tang Y, Nolle FS, Hayden RT, van Belkum A, editors. Molecular Microbiology. Wiley; 2011. pp. 437-52. [DOI: 10.1128/9781555816834.ch27] [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: 11/20/2022]
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12
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Abstract
Mycobacteria include a large number of pathogens. Identification to species level is important for diagnoses and treatments. Here, we report the development of a Web-accessible database of the hsp65 locus sequences (http://msis.mycobacteria.info) from 149 out of 150 Mycobacterium species/subspecies. This database can serve as a reference for identifying Mycobacterium species.
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Chan WW, Murray MC, Tang P, Romney MG. Mycobacterium heckeshornense peritonitis in a peritoneal dialysis patient: a case report and review of the literature. Clin Microbiol Infect 2011; 17:1262-4. [PMID: 21375651 DOI: 10.1111/j.1469-0691.2010.03449.x] [Citation(s) in RCA: 9] [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: 02/06/2023]
Abstract
We report the first case of peritonitis attributed to Mycobacterium heckeshornense. This is a rare, non-tuberculous mycobacterium that has been reported as an aetiological agent in a growing number and widening spectrum of infections.
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Affiliation(s)
- W W Chan
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
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14
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Shen GH, Chiou CS, Hu ST, Wu KM, Chen JH. Rapid identification of the Mycobacterium tuberculosis complex by combining the ESAT-6/CFP-10 immunochromatographic assay and smear morphology. J Clin Microbiol 2011; 49:902-7. [PMID: 21159936 DOI: 10.1128/JCM.00592-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early secretory antigen 6 (ESAT-6) and cell filtrate protein 10 (CFP-10) are two antigens secreted as a complex by the replicating Mycobacterium tuberculosis complex (MTC). Recently, an immunochromatographic assay (ICA) using a monoclonal antibody against the ESAT-6/CFP-10 complex was developed for the purpose of MTC detection. In this study, the efficacy of the assay was tested with 603 BACTEC cultures that were incubated for 3 additional days after positive signals appeared in the BACTEC MGIT 960 system. Bacterial isolates were recovered from these 603 BACTEC cultures, and 332 MTC isolates, 270 nontuberculosis mycobacterial isolates, and 1 Nocardia isolate were identified by using standard biochemical assays. The ESAT-6/CFP-10 assay detected 322 MTC cultures, resulting in a sensitivity of 97% and a specificity of 97.4%. To reduce the false-negative rate and improve the sensitivity, either serpentine cording in an acid-fast bacillus stain of the cultural smear, the ESAT-6/CFP-10 assay, or a combination of both was used for MTC detection. The sensitivity was then increased to 99.1%, and the negative predictive value increased to 98.9%, but the specificity decreased to 94.8% and the positive predictive value decreased to 95.9%. However, a combination of serpentine cording in cultural smears and the positivity of the ICA resulted in the specificity and positive predictive values of 100%. Therefore, BACTEC cultures with both serpentine cording and positivity of the ESAT-6/CFP-10 assay could be reported to contain MTC directly. The ESAT-6/CFP-10 assay may be an alternative of the Capilia assay (MPB64-ICA) as a convenient and cost-effective method for identification of MTC in culture.
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15
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Kim K, Lee H, Lee MK, Lee SA, Shim TS, Lim SY, Koh WJ, Yim JJ, Munkhtsetseg B, Kim W, Chung SI, Kook YH, Kim BJ. Development and application of multiprobe real-time PCR method targeting the hsp65 gene for differentiation of Mycobacterium species from isolates and sputum specimens. J Clin Microbiol 2010; 48:3073-80. [PMID: 20631094 DOI: 10.1128/JCM.00939-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We developed a multiprobe real-time PCR assay targeting hsp65 (HMPRT-PCR) to detect and identify mycobacterial isolates and isolates directly from sputum specimens. Primers and probes for HMPRT-PCR were designed on the basis of the hsp65 gene sequence, enabling the recognition of seven pathogenic mycobacteria, including Mycobacterium tuberculosis, M. avium, M. intracellulare, M. kansasii, M. abscessus, M. massiliense, and M. fortuitum. This technique was applied to 24 reference and 133 clinical isolates and differentiated between all strains with 100% sensitivity and specificity. Furthermore, this method was applied to sputum specimens from 117 consecutive smear-positive patients with smear results of from a trace to 3+. These results were then compared to those obtained using the rpoB PCR-restriction analysis method with samples from cultures of the same sputum specimens. The HMPRT-PCR method correctly identified the mycobacteria in 89 samples (76.0%, 89/117), and moreover, the sensitivity level was increased to 94.3% (50/53) for sputa with an acid-fast bacillus score equal to or greater than 2+. Our data suggest that this novel HMPRT-PCR method could be a promising approach for detecting pathogenic mycobacterial species from sputum samples and culture isolates routinely in a clinical setting.
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Tortoli E, Rogasi PG, Fantoni E, Beltrami C, De Francisci A, Mariottini A. Infection due to a novel mycobacterium, mimicking multidrug-resistant Mycobacterium tuberculosis. Clin Microbiol Infect 2009; 16:1130-4. [PMID: 19832722 DOI: 10.1111/j.1469-0691.2009.03063.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The treatment of multidrug-resistant tuberculosis (TB) requires the use, for long periods, of drugs liable to cause significant side effects. In the case of misdiagnosis of multidrug-resistant TB, the patient is exposed to toxic substances without any benefit. In low-income countries, where the microbiological diagnosis of TB relies on microscopy only, the misdiagnosis of multidrug-resistant TB is very frequent in patients persistently smear-positive despite anti-TB treatment, with the possibility of an infection due to non-tuberculous mycobacteria (NTM) being neglected. The isolation of a mycobacterium from the sputum of a Somali patient apparently confirmed the previous diagnosis of cavitary pulmonary disease. Preliminary investigations led, at first, to the strain being identified as multidrug-resistant Mycobacterium tuberculosis, with findings fully in agreement with the patient's history, which was characterized by repeated interruptions of anti-TB treatment. Thorough phenotypic and genotypic analyses led subsequently to the recognition that the strain was a previously unreported non-tuberculous mycobacterium. The patient, who was unresponsive to the anti-TB treatment, dramatically improved once a drug combination active against NTM was used. A major objective of this article is to alert the medical community to the risk, present also in settings in which sophisticated diagnostic techniques are used, that a cavitary infection due to NTM, and consequently not responding to the anti-TB standard regimen, will be mistaken for multidrug-resistant TB.
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Affiliation(s)
- E Tortoli
- Regional Reference Centre for Mycobacteria, Careggi University Hospital, Florence, Italy.
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Leader BT, Frye JG, Hu J, Fedorka-Cray PJ, Boyle DS. High-throughput molecular determination of salmonella enterica serovars by use of multiplex PCR and capillary electrophoresis analysis. J Clin Microbiol 2009; 47:1290-9. [PMID: 19261787 DOI: 10.1128/JCM.02095-08] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Salmonella enterica is a leading cause of food-borne illness worldwide and is also a major cause of morbidity and mortality in domestic and wild animals. In the current study, a high-throughput molecular assay was developed to determine the most common clinical and nonhuman serovars of S. enterica in the United States. Sixteen genomic targets were identified based on their differential distribution among common serovars. Primers were designed to amplify regions of each of these targets in a single multiplex PCR while incorporating a 6-carboxyfluorescein-labeled universal primer to fluorescently label all amplicons. The fluorescently labeled PCR products were separated using capillary electrophoresis, and a Salmonella multiplex assay for rapid typing (SMART) code was generated for each isolate, based upon the presence or absence of PCR products generated from each target gene. Seven hundred fifty-one blind clinical isolates of Salmonella from Washington State, collected in 2007 and previously serotyped via antisera, were screened with the assay. A total of 89.6% of the isolates were correctly identified based on comparison to a panel of representative SMART codes previously determined for the top 50 most common serovars in the United States. Of the remaining isolates, 6.2% represented isolates that produced a new SMART code for a previously determined serotype, while the final 8.8% were from serotypes not screened in the original panel used to score isolates in the blinded study. This high-throughput multiplex PCR assay allowed simple and accurate typing of the most prevalent clinical serovars of Salmonella enterica at a level comparable to that of conventional serotyping, but at a fraction of both the cost and time required per test.
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Abstract
PURPOSE OF REVIEW The purpose of this article is to review the molecular methods commonly used in medical microbiology as well as to update the clinician as to newer molecular technologies that show promise in the identification of microorganisms as well as evaluation of the presence of virulence factors and antibiotic resistance determinants. RECENT FINDINGS Numerous molecular assays have been developed recently using a variety of technologies. Direct hybridization techniques have allowed analysis of blood culture bottles for organisms such as methicillin-resistant Staphylococcus aureus. Target amplification methods allow postamplification analysis using a variety of technologies depending on the clinical needs for the assay. Postamplification analysis includes methods such as Sanger sequencing, pyrosequencing, reverse hybridization, and Luminex analysis, which are becoming more widely utilized. In the future, whole genome sequencing, mass spectrometry, and microarray analysis may provide a wealth of information that can be used to specifically tailor the treatment of infectious diseases. SUMMARY The implications of current trends in molecular infectious diseases are moving towards high-throughput, simple, array-type technologies that will provide a wealth of data regarding types of organisms present in a sample and the virulence factors/resistance determinants that influence the severity of disease. As a result of these developments, infectious diseases will be more accurately and effectively treated.
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Whipps CM, Matthews JL, Kent ML. Distribution and genetic characterization of Mycobacterium chelonae in laboratory zebrafish Danio rerio. Dis Aquat Organ 2008; 82:45-54. [PMID: 19062752 PMCID: PMC2751615 DOI: 10.3354/dao01967] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During routine screening of zebrafish at a research facility, histological changes consistent with mycobacteriosis were observed, prompting an investigation to determine the background prevalence and distribution of Mycobacterium species throughout the facility. Infection status was evaluated in 240 zebrafish representing 9 genetic lines, using histology, culture and PCR. Environmental sources were also tested for the presence of mycobacteria. Prevalence in zebrafish by culture and PCR was 10% (24/240), 21 of which were TU line fish. All isolates from fish were identified as M. chelonae by hsp65 DNA sequencing; subsequent DNA fingerprinting delineated 3 strains, designated H1E1 (1/24), H1E2 (22/24), and H1E3 (1/24). From external sources, tank or tubing surface biofilms were positive by culture (13/32) with multiple species and strains isolated including M. neoaurum, M. phocaicum, and identical strains of M. chelonae that were found in zebrafish: H1E1 (2/13) and H1E2 (8/13). Comparing diagnostic methods, acid-fast stained histological sections showed substantial agreement with plate culture and PCR for detection of mycobacteria in fish. Observation of granulomas in hematoxylin and eosin-stained sections was a less reliable predictor of mycobacteriosis, as uninfected females with egg-associated inflammation and hyperplasia were misdiagnosed. These data revealed background levels of mycobacteriosis in a healthy and well-managed facility. Infected populations were removed, although the apparent ability for M. chelonae to remain viable in environmental reservoirs may make it difficult to eradicate completely. This highlights the importance of an animal-health monitoring program and good husbandry practices to prevent disease in zebrafish research laboratories.
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Affiliation(s)
- Christopher M Whipps
- State University of New York College of Environmental Science and Forestry, Environmental and Forest Biology, 246 Illick Hall, 1 Forestry Drive, Syracuse, New York 13210, USA.
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Daley P, Petrich A, May K, Luinstra K, Rutherford C, Chedore P, Jamieson F, Smieja M. Comparison of in-house and commercial 16S rRNA sequencing with high-performance liquid chromatography and genotype AS and CM for identification of nontuberculous mycobacteria. Diagn Microbiol Infect Dis 2008; 61:284-93. [DOI: 10.1016/j.diagmicrobio.2008.02.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/19/2008] [Accepted: 02/27/2008] [Indexed: 12/01/2022]
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Abstract
Tests based on nucleic acid amplification can rapidly detect mycobacteria in clinical samples. These appear to be promising and may change how mycobacterial diseases are diagnosed in the future. Utilization of nucleic acid hybridization and DNA sequencing has enabled the identification of mycobacteria to the species level and detection of mutations associated with antimicrobial resistance. Combining nucleic acid amplification with genotypic identification methods allows detection and identification of mycobacteria directly in clinical samples and, to a limited extent, detection of antimicrobial resistance. IFN-gamma-based assays provide results faster than the tuberculin skin test and address many of its shortcomings, and are thus poised to replace the latter in the coming years.
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Affiliation(s)
- Nabin K Shrestha
- Cleveland Clinic, Infectious Diseases/S-32, Cleveland, OH 44195, USA.
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Abstract
New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.
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Affiliation(s)
- Gary W Procop
- Department of Pathology, Jackson Memorial Hospital and University of Miami Miller School of Medicine, Miami, Florida 33136, USA.
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Simmon KE, Pounder JI, Greene JN, Walsh F, Anderson CM, Cohen S, Petti CA. Identification of an emerging pathogen, Mycobacterium massiliense, by rpoB sequencing of clinical isolates collected in the United States. J Clin Microbiol 2007; 45:1978-80. [PMID: 17409204 PMCID: PMC1933107 DOI: 10.1128/jcm.00563-07] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [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: 11/20/2022] Open
Abstract
Mycobacterium massiliense is a rapidly growing mycobacterium that is indistinguishable from Mycobacterium chelonae/M. abscessus by partial 16S rRNA gene sequencing. We sequenced rpoB, sodA, and hsp65 genes from isolates previously identified as being M. chelonae/M. abscessus and identified M. massiliense from isolates from two patients with invasive disease representing the first reported cases in the United States.
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Affiliation(s)
- Keith E Simmon
- Associated Regional and University Pathologists (ARUP) Instititue for Clincal and Experimental Pathology, Salt Lake City, UT 84108, USA.
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