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Dziedzinska R, Okunkova J, Kralik P, Svobodova J, Mala M, Slana I. Identification of and discrimination between the Mycobacterium abscessus complex and Mycobacterium avium complex directly from sputum using quadruplex real-time PCR. J Med Microbiol 2022; 71. [PMID: 36748608 DOI: 10.1099/jmm.0.001611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction. Cystic fibrosis (CF) is a serious disease with multisystemic clinical signs that is easily and frequently complicated by bacterial infection. Recently, the prevalence of nontuberculous mycobacteria as secondary contaminants of CF has increased, with the Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) being the most frequently identified. The MABSC includes subspecies of significant clinical importance, mainly due to their resistance to antibiotics.Gap statement. Sensitive method for early detection and differentiation of MABSC members and MAC complex for use in routine clinical laboratories is lacking. A method based on direct DNA isolation from sputum, using standard equipment in clinical laboratories and allowing uncovering of possible sample inhibition (false negative results) would be required. The availability of such a method would allow accurate and accelerated time detection of MABSC members and their timely and targeted treatment.Aim. To develop a real time multiplex assay for rapid and sensitive identification and discrimination of MABSC members and MAC complex.Methodology. The method of DNA isolation directly from the sputum of patients followed by quadruplex real-time quantitative PCR (qPCR) detection was developed and optimised. The sensitivity and limit of detection (LOD) of the qPCR was determined using human sputum samples artificially spiked with a known amount of M. abscessus subsp. massiliense (MAM).Results. The method can distinguish between MAC and MABSC members and, at the same time, to differentiate between M. abscessus subsp. abscessus/subsp. bolletii (MAAb/MAB) and MAM. The system was verified using 61 culture isolates and sputum samples from CF and non-CF patients showing 29.5 % MAAb/MAB, 14.7 % MAM and 26.2 % MAC. The LOD was determined to be 1 490 MAM cells in the sputum sample with the efficiency of DNA isolation being 95.4 %. Verification of the qPCR results with sequencing showed 100 % homology.Conclusions. The developed quadruplex qPCR assay, which is preceded by DNA extraction directly from patients' sputum without the need for culturing, significantly improves and speeds up the entire process of diagnosing CF patients and is therefore particularly suitable for use in routine laboratories.
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Affiliation(s)
- Radka Dziedzinska
- Laboratory of Neurobiology and Pathological Physiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Jana Okunkova
- Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czechia
| | - Petr Kralik
- Laboratory of Neurobiology and Pathological Physiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | | | - Miriam Mala
- Department of Pediatric Infectious Diseases, Centre of Cystic Fibrosis, University Hospital Brno, Brno, Czechia.,Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Iva Slana
- Department of Animal Origin Food & Gastronomic Sciences, University of Veterinary Sciences Brno, Brno, Czechia
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Bordin A, Pandey S, Coulter C, Syrmis M, Pardo C, Hackett H, Bell SC, Wainwright CE, Nimmo GR, Jennison AV, Clark JE, Whiley DM. Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis. J Med Microbiol 2021; 70. [PMID: 33909552 DOI: 10.1099/jmm.0.001349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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Affiliation(s)
- Amanda Bordin
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Melanie Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Carolyn Pardo
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Hazel Hackett
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C Bell
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Department of Thoracic Medicine, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine Department, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Graeme R Nimmo
- Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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Khan O, Chaudary N. The Use of Amikacin Liposome Inhalation Suspension (Arikayce) in the Treatment of Refractory Nontuberculous Mycobacterial Lung Disease in Adults. Drug Des Devel Ther 2020; 14:2287-2294. [PMID: 32606598 PMCID: PMC7293904 DOI: 10.2147/dddt.s146111] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/26/2020] [Indexed: 12/30/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) can cause and perpetuate chronic inflammation and lung infection. Despite having the diagnostic criteria, as defined by the American Thoracic Society (ATS) and Infectious Diseases Society of America (IDSA), clinicians find it challenging to diagnose and treat NTM-induced lung disease. Inhaled antibiotics are suitable for patients with lung infection caused by Pseudomonas aeruginosa and other organisms, but until recently, their utility in NTM-induced infection was not established. The most common NTM pathogens identified are the slow-growing Mycobacterium avium complex (MAC) and the rapid-growing M. abscessus complex (MABSC), both of which include several subspecies. Other less commonly isolated species include M. kansasii, M. simiae, and M. fortuitum. NTM strains are frequently more resistant than what is found in bacterial sputum cultures. Until recently, there was no approved inhaled antibiotic therapy for patients who were culture positive for pulmonary NTM infection. Of late, inhaled amikacin has been under investigation for the treatment of NTM-induced pulmonary infection. The FDA approved Arikayce (amikacin liposome inhalation suspension or ALIS) based on results from the ongoing Phase 3 CONVERT trial. In this study, the use of Arikayce met its primary endpoint of sputum culture conversion by the sixth month of treatment. The addition of Arikayce to guideline-based therapy led to negative sputum cultures for NTM by month 6 in 29% of patients compared to 8.9% of patients treated with guideline-based therapy alone. The effectiveness of Arikayce holds promise. However, due to limited data on Arikayce's safety, it is currently useful only for a specific population, particularly patients with refractory NTM-induced lung disease. Future trials must verify the target group and endorse the clinical benefits of Arikayce.
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Affiliation(s)
- Omer Khan
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Nauman Chaudary
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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