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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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Clinical characteristics and imaging features of patients with nontuberculous mycobacteria in a tertiary care center. J Clin Tuberc Other Mycobact Dis 2022; 26:100294. [PMID: 35028436 PMCID: PMC8739879 DOI: 10.1016/j.jctube.2021.100294] [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] [Indexed: 11/23/2022] Open
Abstract
Background Non-tuberculous mycobacteria (NTM) are ubiquitous organisms that occasionally causes invasive diseases in humans, but they are under-reported in Saudi Arabia. We aimed to describe NTM infections and apply the American Thoracic Society/Infectious Diseases Society of America ATS/IDSA criteria. Method Positive laboratory reports for NTM between January 2006 and December 2017 were retrospectively reviewed, and then classified into respiratory and non-respiratory specimens. ATS/IDSA criteria were applied to all respiratory specimens. Host status, clinical presentation, species identification, imaging, treatment, and outcome data were collected using a standardized form and analyzed. Cases with duplication or incomplete data were excluded. Results 183 unique patients with positive NTM culture were included. Median age was 52 years and males represented 59%. Majority of cases were in the respiratory specimens group (n = 146), of which only 15 cases have met the ATS/IDSA criteria. Overall, cases were primarily known to have non-immunocompromising condition but 27% had either an active malignancy (n = 35), HIV (n = 13), or primary immunodeficiency (n = 8). 68.3% of cases presented with respiratory symptoms with or without fever. Among the identified NTM species (51.9%), slowly growing NTM were predominant. Anti-NTM therapy was provided in only 22.4% of this cohort. Death was documented only in 5 cases; all were in the respiratory group and were not treated. Conclusion Though uncommon to isolate, only one in every ten respiratory NTM isolates was found potentially true pathogen in a single center in Saudi Arabia. Future studies on NTM prevalence in Saudi Arabia are recommended.
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Guan Q, Garbati M, Mfarrej S, AlMutairi T, Laval T, Singh A, Fagbo S, Smyth A, Browne J, urRahman M, Alruwaili A, Hoosen A, Meehan C, Nakajima C, Suzuki Y, Demangel C, Bhatt A, Gordon S, AlAsmari F, Pain A. Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense. NAR Genom Bioinform 2021; 3:lqab070. [PMID: 34396095 PMCID: PMC8356964 DOI: 10.1093/nargab/lqab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 01/08/2023] Open
Abstract
Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.
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Affiliation(s)
- Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | - Musa Garbati
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | | | - Thomas Laval
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, 75205 CEDEX 13, Paris, France
| | | | | | | | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 W6F6, Ireland
| | | | - Alya Alruwaili
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Anwar Hoosen
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Conor J Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, BD7 1AZ, UK
| | - Chie Nakajima
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Yasuhiko Suzuki
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | | | | | | | | | - Arnab Pain
- To whom correspondence should be addressed. Tel: +966 54 470 0687;
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Alenazi TH, Alanazi BS, Alsaedy A, Khair A, Solomon R, Al Johani SM. Mycobacterium riyadhense as the opportunistic infection that lead to HIV diagnosis: A report of 2 cases and literature review. J Infect Public Health 2018; 12:285-288. [PMID: 29884324 DOI: 10.1016/j.jiph.2018.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection usually presents with a wide range of manifestations. Although HIV patients are prone to pulmonary infections by opportunistic pathogens in the late stage of AIDS, manifesting the disease with pulmonary infections caused by Mycobacterium riyadhense (newly identified non-tuberculous mycobacteria) is extremely rare with only one case reported in the literature. We are describing two previously healthy patients who presented with M. riyadhense lung infection and were subsequently found to have HIV, illustrating the need for considering the possibility M. riyadhense lung infection as a presenting illness of HIV.
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Affiliation(s)
- Thamer H Alenazi
- Infection Prevention and Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Bashayer S Alanazi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alsaedy
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Division of Infectious Diseases, Department of Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulmoneim Khair
- Pulmonary Division, Department of Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Rifat Solomon
- Microbiology Division, Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Sameera M Al Johani
- Microbiology Division, Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Varghese B, Enani MA, Althawadi S, Johani S, Fernandez GM, Al-Ghafli H, Al-Hajoj S. Mycobacterium riyadhense in Saudi Arabia. Emerg Infect Dis 2018; 23:1732-1734. [PMID: 28930028 PMCID: PMC5621544 DOI: 10.3201/eid2310.161430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We explored in detail the nationwide existence of Mycobacterium riyadhense in Saudi Arabia. In 18 months, 12 new cases of M. riyadhense infection were observed, predominantly among Saudi nationals, as a cause of pulmonary disease. M. riyadhense may be emerging as a more common pathogen in Saudi Arabia.
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Nontuberculous Mycobacteria in Saudi Arabia and Gulf Countries: A Review. Can Respir J 2017; 2017:5035932. [PMID: 28348502 PMCID: PMC5350348 DOI: 10.1155/2017/5035932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/05/2017] [Accepted: 02/01/2017] [Indexed: 01/15/2023] Open
Abstract
Nontuberculous Mycobacteria (NTM) are causing growing health problems worldwide. This is indicated by an increasing amount of scientific reports showing not only well-identified species reemerging but also emergence of new species. The emergence and reemergence of NTM are particularly worrying in developing countries due to scarce published data and improper identification. Here we aimed to examine the main epidemiological aspects and diagnostic challenges associated with NTM in countries of the Gulf Cooperation Council (GCC) and compare these findings to the international arena findings. Data revealed that countries of the GCC are largely dominated by rapidly growing mycobacteria species such as M. fortuitum (29%) and M. abscessus (17%) with high rate of definitive respiratory diseases. On the other hand, most of the developed countries are dominated by slowly growing mycobacteria such as MAC, M. kansasii, and M. gordonae. More efforts are needed, however, to gain insights into NTM issues in countries of the GCC.
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Abstract
Mycobacterium riyadhense is a newly described slowly growing, non-tuberculous mycobacterium species. We describe 2 new cases of Mycobacterium riyadhense infections presenting with extra-pulmonary involvement, and reviewed all previously reported cases in the literature. We also describe the spectrum of the disease and explore treatment options based on the experience with the current and previously reported cases.
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Affiliation(s)
- Mustafa M Saad
- Division of Infectious Diseases, Prince Sultan Military Medical City, PO Box 9789 A-55, Riyadh 11159, Kingdom of Saudi Arabia. Tel. +966 (11) 4777714 Ext 88231. E-mail.
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A Case of Mycobacterium riyadhense in an Acquired Immune Deficiency Syndrome (AIDS) Patient with a Suspected Paradoxical Response to Antituberculosis Therapy. Case Rep Infect Dis 2016; 2016:5908096. [PMID: 27703819 PMCID: PMC5039294 DOI: 10.1155/2016/5908096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/02/2016] [Accepted: 08/29/2016] [Indexed: 11/25/2022] Open
Abstract
A 30-year-old male patient with acquired immune deficiency syndrome (AIDS) on highly active antiretroviral therapy (HAART) presented with clinical picture suggestive of pulmonary tuberculosis. He was commenced on antituberculosis therapy (ATT) with signs of improvement. Then he developed cervical lymph node abscess which was drained. Steroid was started for presumed paradoxical response to ATT which results in clinical regression. The culture result revealed Mycobacterium riyadhense. This report addresses the rarity of this bacteria in medical literature. It reviews clinical presentations and medical treatment particularly in the setting of coinfections.
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Microbiological features and clinical relevance of new species of the genus Mycobacterium. Clin Microbiol Rev 2015; 27:727-52. [PMID: 25278573 DOI: 10.1128/cmr.00035-14] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are present in the environment, mainly in water, and are occasionally responsible for opportunistic infections in humans. Despite the fact that NTM are characterized by a moderate pathogenicity, the diseases caused by NTM at various body sites are increasing on a worldwide level. Among over 150 officially recognized NTM species, only two or three dozen are familiar to clinicians, and even to most microbiologists. In this paper, approximately 50 new species described in the last 8 years are reviewed, and their role in human infections is assessed on the basis of reported clinical cases. The small number of reports concerning most of the "new" mycobacterial species is responsible for the widespread conviction that they are very rare. Their role is actually largely underestimated, mainly because they often remain unrecognized and misidentified. Aiming to minimize such bias, emphasis has been placed on more common identification pitfalls. Together with new NTM, new members of the Mycobacterium tuberculosis complex described in the last few years are also an object of the present review.
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Velayati AA, Rahideh S, Nezhad ZD, Farnia P, Mirsaeidi M. Nontuberculous mycobacteria in Middle East: Current situation and future challenges. Int J Mycobacteriol 2015; 4:7-17. [PMID: 26655192 DOI: 10.1016/j.ijmyco.2014.12.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/07/2014] [Accepted: 12/16/2014] [Indexed: 11/30/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are a diverse group of bacterial species that are distributed in the environment. Many of these environmental bacteria can cause disease in humans. The identification of NTM in environmental sources is important for both clinical and epidemiological purposes. In this study, the distribution of NTM species from environmental and clinical samples in the Middle East was reviewed. In order to provide an overview of NTM, as well as recent epidemiological trends, all studies addressing NTM in the Middle East from 1984 to 2014 were reviewed. A total of 96 articles were found, in which 1751 NTM strains were isolated and 1084 of which were obtained from clinical samples, 619 from environmental samples and 48 were cited by case reports. Mycobacterium fortuitum was the most common rapid growing mycobacteria (RGM) isolated from both clinical (269 out of 447 RGM; 60.1%) and environmental (135 out of 289 RGM; 46.7%) samples. Mycobacterium avium complex (MAC) was the most common slow growing mycobacteria (SGM) isolated from clinical samples (140 out of 637 SGM; 21.9%). An increasing trend in NTM isolation from the Middle East was noted over the last 5years. This review demonstrates the increasing concern regarding NTM disease in the Middle East, emphasizing the need for regional collaboration and coordination in order to respond appropriately.
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Affiliation(s)
- Ali Akbar Velayati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sanaz Rahideh
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Derakhshani Nezhad
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Illinois at Chicago, USA.
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Bañuls AL, Thomas F, Renaud F. Of parasites and men. INFECTION GENETICS AND EVOLUTION 2013; 20:61-70. [PMID: 23954419 DOI: 10.1016/j.meegid.2013.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 01/14/2023]
Abstract
The living world has evolved and is evolving through interspecific relationships between organisms. The diversity of these interactions is enormous going from mutualism to parasitism. Humans live with a multitude of microorganisms, essential for their biology. However, interactions are not always advantageous. Indeed, many organisms might become pathogens, such as the Plasmodium species, the causative agents of malaria. Like many other microorganisms, they are «Machiavellian» in their capacity to elaborate a range of reproduction strategies, giving them a huge advantage in terms of adaptation. Here, we discuss the role played by parasites in the ecology and evolution of living organisms and particularly of humans. In the study of infectious diseases, humans are legitimately the focal point, although they represent only one ecosystem among many others and not taking this into account certainly biases our global view of the system. Indeed, we know only a minimal fraction of the microorganisms we live with. However, parasites have shaped and are still shaping the human genome. Several genetic signatures are the proofs of the selection pressures by parasites that humankind has endured during its evolution. But, ultimately, what are the solutionsfor living with pathogens? Should we eradicate them or should we learn how to control and manage them?
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Affiliation(s)
- Anne-Laure Bañuls
- Laboratoire MIVEGEC (UMR CNRS 5290-IRD 224 - Universités Montpellier 1 et 2), Institut de Recherche pour le Développement (IRD), PO Box 64501, 34394 Montpellier, France.
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Choi JI, Lim JH, Kim SR, Lee SH, Park JS, Seo KW, Jeon JB, Jeong J. Lung infection caused by Mycobacterium riyadhense confused with Mycobacterium tuberculosis: the first case in Korea. Ann Lab Med 2012; 32:298-303. [PMID: 22779073 PMCID: PMC3384813 DOI: 10.3343/alm.2012.32.4.298] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/10/2012] [Accepted: 05/17/2012] [Indexed: 11/19/2022] Open
Abstract
A slowly growing, non-chromogenic mycobacterial strain was isolated from sputum and bronchial lavage fluid samples of a patient presenting with productive cough, blood-tinged sputum, low-grade fever, and weakness. A positive acid-fast bacilli sputum smear result prompted the initiation of an anti-tuberculosis regimen. Multiplex real-time PCR showed a negative result for Mycobacterium tuberculosis complex and a positive result for nontuberculous mycobacteria. The DNA chip test confirmed this organism as a member of the genus Mycobacterium, but could not specify the species. Interestingly, the mycolic acid patterns obtained by HPLC nearly overlapped with those of M. simulans. The sequences of the Mycobacterium 16S rRNA gene and 16S-23S internal transcribed spacer region were unique and were found to have 100% similarity with those of M. riyadhense. After a review of the literature, we report this case as the first Korean case of M. riyadhense lung infection.
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Affiliation(s)
- Jung-In Choi
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Korea
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