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Caldera JR, Anikst V, Gray H, Tsan A, Sono R, Yang S. Performance Evaluation of a Commercial Automated Library Preparation System for Clinical Microbial Whole-Genome Sequencing Assays. J Mol Diagn 2024; 26:719-726. [PMID: 38851385 DOI: 10.1016/j.jmoldx.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/15/2024] [Accepted: 05/10/2024] [Indexed: 06/10/2024] Open
Abstract
Next-generation sequencing (NGS) has proven clinical utility on disease management and serves as an important tool for genomic surveillance. Currently, hurdles surrounding its implementation, namely the complex and demanding analytical workflows, have impeded its widespread use in many laboratories. To address this challenge, the UCLA Molecular Microbiology and Pathogen Genomics Laboratory evaluated the performance of the Tecan MagicPrep NGS system, a commercial automated solution for library preparation for clinical whole-genome sequencing assays, against the Illumina Nextera DNA Flex Library Prep. Using 35 unique organisms (28 bacteria and 7 fungi) for various clinical applications, including microbial identification and genomic characterization, we compared the quantity and quality of the prepared libraries and the resulting sequences, and concordance of the overall results. We also assessed the impact of its implementation on laboratory workflow. The MagicPrep NGS produced higher library concentrations with smaller sizes, and correspondingly, higher molarity. Quality metrics of the sequences, however, demonstrated no significant impact on the overall results, producing 100% concordance with the reference method. Importantly, workflow analysis showed 5 hours less hands-on time per run with more flexibility. This evaluation study indicates that performance of the MagicPrep NGS is comparable to the Nextera DNA Flex with the added benefit of improving workflow efficiency and reducing labor for performing routine clinical microbial whole-genome sequencing tests.
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Affiliation(s)
- J R Caldera
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California
| | - Victoria Anikst
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California
| | - Hannah Gray
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California
| | - Allison Tsan
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California
| | - Reiri Sono
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA Health and David Geffen School of Medicine, Los Angeles, California.
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Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024:10.1007/s40291-024-00727-9. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
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Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Johanis M, Cheema KS, Young PA, Bae GH. Bilateral Jaw Mycobacterium Abscessus Mimicking Actinomycosis: A Postoperative Complication of Wisdom Teeth Extraction. Cureus 2024; 16:e62336. [PMID: 39006726 PMCID: PMC11246195 DOI: 10.7759/cureus.62336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
The incidence of nontuberculous mycobacteria infections has surged over recent decades. Mycobacterium abscessus is one example that can present unique diagnostic challenges due to its variable antibiotic resistance profile and its clinical similarities to Actinomycoses israelii in postodontogenic infections. The authors report a case of a 22-year-old healthy female presenting with bilateral mandibular nodules following wisdom teeth extraction. After a presumptive diagnosis of actinomycosis, cultures revealed a Mycobacterium abscessus infection susceptible to macrolides. Magnetic resonance imaging depicted bilateral sinus tracts without osteomyelitis. The patient opted for dual antibiotic therapy, consisting of azithromycin and omadacycline, without surgical intervention. Given her clinical and radiographic improvement after three months, the patient elected to continue dual antibiotic therapy for 12 months with appropriate clinical and radiographic monitoring. This case underscores the importance of early microbial cultures to guide diagnosis and treatment, particularly considering Mycobacterium abscessus's similarities with other pathogens and its variable macrolide susceptibility due to genetic mutations. As highlighted in this case, clinicians must successfully differentiate between and appropriately treat various nontuberculous mycobacteria.
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Affiliation(s)
- Michael Johanis
- Department of Dermatology, Stanford University School of Medicine, Palo Alto, USA
| | - Karan S Cheema
- School of Public Health, Brown University, Providence, USA
| | - Peter A Young
- Department of Dermatology, Kaiser Permanente, Sacramento, USA
| | - Gordon H Bae
- Department of Dermatology, Stanford University School of Medicine, Palo Alto, USA
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Ren W, Mao Y, Li S, Gao B, Fu X, Liu X, Zhu P, Shang Y, Li Y, Ma B, Sun L, Xu J, Pang Y. Rapid Mycobacterium abscessus antimicrobial susceptibility testing based on antibiotic treatment response mapping via Raman Microspectroscopy. Ann Clin Microbiol Antimicrob 2023; 22:94. [PMID: 37904155 PMCID: PMC10617219 DOI: 10.1186/s12941-023-00644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
OBJECTIVES Antimicrobial susceptibility tests (ASTs) are pivotal tools for detecting and combating infections caused by multidrug-resistant rapidly growing mycobacteria (RGM) but are time-consuming and labor-intensive. DESIGN We used a Mycobacterium abscessus-based RGM model to develop a rapid (24-h) AST from the beginning of the strain culture, the Clinical Antimicrobials Susceptibility Test Ramanometry for RGM (CAST-R-RGM). The ASTs obtained for 21 clarithromycin (CLA)-treated and 18 linezolid (LZD)-treated RGM isolates. RESULTS CAST-R-RGM employs D2O-probed Raman microspectroscopy to monitor RGM metabolic activity, while also revealing bacterial antimicrobial drug resistance mechanisms. The results of clarithromycin (CLA)-treated and linezolid (LZD)-treated RGM isolates exhibited 90% and 83% categorical agreement, respectively, with conventional AST results of the same isolates. Furthermore, comparisons of time- and concentration-dependent Raman results between CLA- and LZD-treated RGM strains revealed distinct metabolic profiles after 48-h and 72-h drug treatments, despite similar profiles obtained for both drugs after 24-h treatments. CONCLUSIONS Ultimately, the rapid, accurate, and low-cost CAST-R-RGM assay offers advantages over conventional culture-based ASTs that warrant its use as a tool for improving patient treatment outcomes and revealing bacterial drug resistance mechanisms.
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Affiliation(s)
- Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuli Mao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Bo Gao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Liu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zhu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Single-Cell Biotech, Co. Ltd, Qingdao, Shandong, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuandong Li
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyang Sun
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jian Xu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
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Buckwalter SP, Olson SL, Fida M, Epperson LE, Hasan NA, Khare R, Strong M, Wengenack NL. Mycobacterium abscessus subspecies identification using the Deeplex Myc-TB targeted NGS assay. J Clin Microbiol 2023; 61:e0048923. [PMID: 37732763 PMCID: PMC10595067 DOI: 10.1128/jcm.00489-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Affiliation(s)
| | - Sara L. Olson
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Madiha Fida
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Reeti Khare
- Mycobacteriology Laboratory, Advanced Diagnostic Laboratories, National Jewish Health, Denver, Colorado, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Nancy L. Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Sukmongkolchai S, Petsong S, Oudomying N, Prommi A, Payungporn S, Usawakidwiree W, Wongjarit K, Suwanpimolkul G, Faksri K, Suankratay C, Rotcheewaphan S. Clinical characteristics and drug susceptibility profiles of Mycobacterium abscessus complex infection at a medical school in Thailand. Ann Clin Microbiol Antimicrob 2023; 22:87. [PMID: 37735687 PMCID: PMC10515245 DOI: 10.1186/s12941-023-00637-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
OBJECTIVES This study investigated the differences in epidemiological and clinical data, and antimicrobial susceptibilities among different subspecies of Mycobacterium abscessus complex (MABSC) clinical isolates at a medical school in Thailand. METHODS A total of 143 MABSC clinical isolates recovered from 74 patients were genotypically analyzed for erm(41), rrl, and rrs mutations, and antimicrobial susceptibilities were determined using a broth microdilution method. Patient characteristics and clinical outcomes were reviewed from the medical records. RESULTS Seventy-four patients were infected with 28/74 (37.8%) M. abscessus subspecies abscessus (MAB), 43/74 (58.1%) M. abscessus subsp. massiliense (MMA), and 3/74 (4.1%) M. abscessus subsp. bolletii (MBO). The clinical findings and outcomes were generally indistinguishable between the three subspecies. All three subspecies of MABSC clinical isolates exhibited high resistance rates to ciprofloxacin, doxycycline, moxifloxacin, TMP/SMX, and tobramycin. MAB had the highest resistance rates to clarithromycin (27.8%, 20/72) and amikacin (6.9%, 5/72) compared to MBO and MMA, with p < 0.001 and p = 0.004, respectively. In addition, the rough morphotype was significantly associated with resistance to amikacin (8.9%, 5/56), clarithromycin (26.8%, 15/56), and imipenem (76.8%, 43/56) (p < 0.001), whereas the smooth morphotype was resistant to linezolid (57.1%, 48/84) (p = 0.002). In addition, T28 of erm(41), rrl (A2058C/G and A2059C/G), and rrs (A1408G) mutations were detected in 87.4% (125/143), 16.1% (23/143), and 9.1% (13/143) of MABSC isolates, respectively. CONCLUSIONS Three MABSC subspecies caused a variety of infections in patients with different underlying comorbidities. The drug susceptibility patterns of the recent circulating MABSC strains in Thailand were different among the three MABSC subspecies and two morphotypes.
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Affiliation(s)
- Songkiat Sukmongkolchai
- Medical Microbiology, Interdisciplinary and International Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Suthidee Petsong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nont Oudomying
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chulalongkorn University International Medical Program (CU-MEDi), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ajala Prommi
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Warat Usawakidwiree
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kanphai Wongjarit
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Gompol Suwanpimolkul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Chusana Suankratay
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suwatchareeporn Rotcheewaphan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Ranson EL, Tsevat RK, von Bredow B, Kamau E, Yang S, Prabaker KK. Catheter-Related Bloodstream Infection Caused by Mycolicibacterium iranicum, California, USA. Emerg Infect Dis 2023; 29:217-219. [PMID: 36573647 PMCID: PMC9796217 DOI: 10.3201/eid2901.220851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We describe a case of catheter-related bacteremia caused by Mycolicibacterium iranicum in the United States. The case highlights the value of using next-generation sequencing to identify infrequent and emerging pathogens and the challenges associated with choosing appropriate treatments because of limited knowledge of drug resistance mechanisms in those emerging pathogens.
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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Rapid Detection of Clarithromycin and Amikacin Resistance in Mycobacterium abscessus Complex by High-Resolution Melting Curve Analysis. Microbiol Spectr 2022; 10:e0057422. [PMID: 35638787 PMCID: PMC9241889 DOI: 10.1128/spectrum.00574-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The emergence of Mycobacterium abscessus complex (MABC) infection is the most noteworthy health care problem. Clarithromycin (CLA) and amikacin (AMK) constitute the cornerstone of treatment for patients infected with MABC; thus, early detection of resistance to these two drugs is essential for formulating effective therapeutic regimens. In the present study, we aimed to validate the use of MeltPro MAB assay, a melting curve analysis with dually labeled probes, on a set of clinical isolates to detect CLA and AMK resistance. A total of 103 clinical MABC strains were collected in our analysis, including 76 strains of M. abscessussubsp. Abscessus (MAA) and 27 strains of M. abscessussubsp. Massiliense (MAM). In vitro susceptibility testing revealed that two isolates exhibited intrinsic CLA resistance by harboring A2270T mutation in rrl, and inducible resistance was noted in 42 isolates. Additionally, two MAA isolates with erm(41)T28 genotype were susceptible to CLA. Notably, we found three out of 44 isolates had two melting curve peaks, representing the simultaneous presence of mutant and the wild type in these specimens. In contrast, no known mutations were identified in six AMK-resistant isolates. Further analysis revealed that MeltPro yielded 100% and 96.67% sensitivity and specificity for detecting CLA resistance. In summary, this study firstly demonstrates that MeltPro is a promising diagnostic for early detection of CLA resistance for MABC isolates, which significantly improves the turnaround time within 2 h. Approximate two fifths of MABC isolates are resistant to CLA by 23S rRNA mutation or its methylation, emphasizing the urgent need for early detection of CLA resistance prior to empirical treatment of MABC infections. IMPORTANCEMycobacterium abscessus complex (MABC) has attracted increasing attention due to the numerous cases of infection. This pathogen is notorious for its intrinsic drug resistance, which complicates clinical management of patients with MABC infections. Clarithromycin (CLA) and amikacin (AMK) are the cornerstone of treatment regimens for MABC. Herein, our data firstly demonstrates that MeltPro is a promising diagnostic for early detection of CLA resistance for MABC isolates. The high frequency of CLA-resistant MABC isolates in China emphasizes the urgent need for early detection of CLA resistance prior to empirical treatment of MABC infections.
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11
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Zhang Z, Wang W, Wang Y, Xue Z, Li S, Pang Y. Inducible Resistance to Amikacin in Mycobacterium abscessus Isolated in Beijing, China. Infect Drug Resist 2022; 15:2287-2291. [PMID: 35510159 PMCID: PMC9059872 DOI: 10.2147/idr.s357887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
We aimed to determine the prevalence of amikacin (AMK) resistance of clinical Mycobacterium abscessus (MAB) isolates and to investigate if AMK resistance was induced by AMK exposure. A total of 75 MAB isolates underwent susceptibility testing for AMK after 3 and 14 days of incubation, respectively. The partial fragment of the rrs gene conferring AMK resistance was sequenced. The MIC values for AMK ranged from 0.5 to 128 μg/mL, with MIC50 and MIC90 values of 2 and 32 μg/mL, respectively. In addition, 9.3% of isolates (7/75) were resistant to AMK, all of which harbored a mutation within the rrs locus, including six with A1408G mutation and one with a C1409T mutation. Of note, the MICs of three isolates were significantly increased from 2 μg/mL to 64 μg/mL (one isolate) and 2 μg/mL to 128 μg/mL (two isolates), suggesting that three of the MAB isolates had inducible resistance to AMK. In conclusion, our data demonstrate that approximately one-tenth of clinical MAB isolates in Beijing harbored AMK resistance due to the acquisition of rrs mutations. Additionally, we firstly identified that intrinsic AMK resistance is inducible in MAB isolates, highlighting the urgent need to establish a proper method for the in vitro detection of AMK susceptibility in MAB.
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Affiliation(s)
- Zhijian Zhang
- Department of Respiratory and Critical Care Medicine, the Second Medical Center of Chinese PLA General Hospital, Beijing, 100036, People’s Republic of China
| | - Wei Wang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Yufeng Wang
- Innovation Alliance on Tuberculosis Diagnosis and Treatment, Beijing, 101149, People’s Republic of China
| | - Zhongtan Xue
- Innovation Alliance on Tuberculosis Diagnosis and Treatment, Beijing, 101149, People’s Republic of China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
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12
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Chawla R, von Bredow B, Deville J, Yang S. Reinfection or relapse? A case study of whole genome sequencing guided genomic characterization of Mycobacterium abscessus chronic infection in a cystic fibrosis patient. IDCases 2022; 28:e01491. [PMID: 35369567 PMCID: PMC8968000 DOI: 10.1016/j.idcr.2022.e01491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/27/2022] [Accepted: 03/27/2022] [Indexed: 11/25/2022] Open
Abstract
A 7-year-old cystic fibrosis patient with increased cough, new pulmonary infiltrate, and declining pulmonary function was diagnosed with clarithromycin resistant Mycobacterium abscessus infection. Treatment was initiated with clofazimine, linezolid and cefoxitin; she responded well to therapy and achieved microbiological clearance after completion of 12-month treatment. One year later, she had re-emergence of worsening symptoms and her sputum culture again grew clarithromycin resistant M. abscessus. Using a laboratory developed whole genome sequencing (WGS) test, the bacterium was determined to be the same strain with the same resistance mechanisms, indicating a relapse. This was deemed a critical element of clinical information, as the isolation of a genetically distinct organism would have indicated a new infection and would have served as evidence that a 12-month regimen was likely sufficient to achieve eradication. The confirmation of a relapse prompted the prolongation of the therapy plan to a goal of 24 months. Reinfection and relapse are great challenges in patients with cystic fibrosis who may acquire new strain of M. abscessus from the environment, may harbor multiple subpopulations of bacteria, or may have persistent infections but intermittent bacteria shedding that could not be eradicated. WGS has emerged as a powerful molecular tool to accurately differentiate re-infection from relapse thus solving this conundrum.
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Affiliation(s)
- Rachit Chawla
- University of California, Los Angeles, CA, USA.,Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jaime Deville
- UCLA Mattel Children's Hospital, Los Angeles, CA, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
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Solanki P, Lipman M, McHugh TD, Satta G. Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria. Front Microbiol 2022; 13:1044515. [PMID: 36523832 PMCID: PMC9745125 DOI: 10.3389/fmicb.2022.1044515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are opportunistic pathogens commonly causing chronic, pulmonary disease which is notoriously hard to treat. Current treatment for NTM infections involves at least three active drugs (including one macrolide: clarithromycin or azithromycin) over 12 months or longer. At present there are limited phenotypic in vitro drug susceptibility testing options for NTM which are standardised globally. As seen with tuberculosis, whole genome sequencing has the potential to transform drug susceptibility testing in NTM, by utilising a genotypic approach. The Comprehensive Resistance Prediction for Tuberculosis is a database used to predict Mycobacterium tuberculosis resistance: at present there are no similar databases available to accurately predict NTM resistance. Recent studies have shown concordance between phenotypic and genotypic NTM resistance results. To benefit from the advantages of whole genome sequencing, further advances in resistance prediction need to take place, as well as there being better information on novel drug mutations and an understanding of the impact of whole genome sequencing on NTM treatment outcomes.
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Affiliation(s)
- Priya Solanki
- UCL-TB and UCL Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Marc Lipman
- UCL-TB and UCL Respiratory, University College London, London, United Kingdom.,Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Timothy D McHugh
- UCL-TB and UCL Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Giovanni Satta
- UCL-TB and UCL Centre for Clinical Microbiology, University College London, London, United Kingdom
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14
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Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory: A Step Forward, but Not an End-All. J Mol Diagn 2021; 23:1415-1421. [PMID: 34756275 DOI: 10.1016/j.jmoldx.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
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15
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Dohál M, Porvazník I, Solovič I, Mokrý J. Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections. Microorganisms 2021; 9:microorganisms9112237. [PMID: 34835363 PMCID: PMC8621650 DOI: 10.3390/microorganisms9112237] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.
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Affiliation(s)
- Matúš Dohál
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
- Correspondence: ; Tel.: +42-19-0252-4199
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Juraj Mokrý
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
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