1
|
Zuo Z, Zheng R, Li F, Xu A, Shi J. Coinfection of Cytomegalovirus, Pneumocystis jirovecii pneumonia, COVID-19, and Mycobacterium colombiense in an AIDS patient: A case report. Heliyon 2024; 10:e31729. [PMID: 38867990 PMCID: PMC11167289 DOI: 10.1016/j.heliyon.2024.e31729] [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: 02/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
We present an AIDS patient coinfected with Cytomegalovirus, Pneumocystis jirovecii pneumonia, nontuberculous mycobacteria, and COVID-19, who finally recovered from the coinfection. The 36-year-old man had two hospitalizations. In the first hospitalization, the patient was diagnosed with Cytomegalovirus, Pneumocystis jirovecii pneumonia, HIV, and COVID-19 quickly and accurately, and the corresponding treatment worked well. The second hospitalization can be divided into four stages: (1) Persistent fever period; (2) Persistent fever and Pulmonary Progression; (3) ICU period; and (4) Pneumothorax period. During the second hospitalization, the diagnosis of Mycobacterium colombiense was hard because the NGS, acid-fast bacilli, and culture of vomit, sputum, and bronchoalveolar lavage fluid were all negative. Still, we detected acid-fast bacilli in the blood mycobacterium culture. In conclusion, we report a severe pneumonia AIDS patient coinfected with Cytomegalovirus, Pneumocystis jirovecii pneumonia, COVID-19, and Mycobacterium colombiense who finally recovered from the disease. Nontuberculous mycobacteria infection is common in HIV patients, but bronchoalveolar lavage fluid NGS cannot identify nontuberculous mycobacteria in our report. Traditional blood culture was useful in detecting acid-fast bacilli in our study and then detecting the pathogens with NGS. Combining traditional microbial culture and emerging rapid NGS methods is more conducive to clinical diagnosis and treatment.
Collapse
Affiliation(s)
- Zhongbao Zuo
- Department of Clinical Laboratory, Hangzhou Xixi Hospital, 310023, Zhejiang, China
| | - Rongrong Zheng
- The Second Department of Infectious Diseases, Hangzhou Xixi Hospital, 310023, Zhejiang, China
| | - Feng Li
- The Second Department of Infectious Diseases, Hangzhou Xixi Hospital, 310023, Zhejiang, China
| | - Aifang Xu
- Department of Clinical Laboratory, Hangzhou Xixi Hospital, 310023, Zhejiang, China
| | - Jinchuan Shi
- The Second Department of Infectious Diseases, Hangzhou Xixi Hospital, 310023, Zhejiang, China
| |
Collapse
|
2
|
Qin J, Tang G. Disseminated Mycobacterium colombiense infection mimicking malignancy: A case report. Heliyon 2024; 10:e30567. [PMID: 38726108 PMCID: PMC11079310 DOI: 10.1016/j.heliyon.2024.e30567] [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: 01/13/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Mycobacterium colombiense, an infrequently reported non-tuberculous mycobacterium, is characterized by its slow-growing nature and capacity to simulate malignancies in clinical presentation. This report details a case of disseminated M. colombiense infection initially misidentified as cancer due to atypical symptoms, negative etiological tests, and imaging suggestive of a neoplastic disease. However, comprehensive diagnostic investigations, including a bone marrow biopsy and flow cytometry analysis, excluded malignancy as the diagnosis. The patient subsequently developed palpable masses, from which a definitive diagnosis was made using metagenomic Next-Generation Sequencing (mNGS) and culture of aspirate. A regimen of clarithromycin, ethambutol, rifampin, and amikacin was administered, leading to substantial improvement and resumption of activities at the eight-month follow-up. This case highlights the diagnostic challenges posed by the nonspecific clinical presentation of disseminated M. colombiense infection and the importance of rigorous investigation to avoid grave misdiagnosis and treatment delays.
Collapse
Affiliation(s)
- Jiayuan Qin
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Guangmin Tang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
3
|
Guo Y, Li X, Xiao Q, Yang J, Tao R, Xu L, Zhu B. Mycobacterium colombiense Pneumonia in HIV-Infected Patients: Three Case Reports and a Literature Review. Infect Drug Resist 2023; 16:7767-7773. [PMID: 38148773 PMCID: PMC10750772 DOI: 10.2147/idr.s441083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023] Open
Abstract
Background Mycobacterium colombiense pneumonia in HIV-infected patients is relatively unusual but is associated with a high mortality rate, as well as high rates of misdiagnosis and delayed diagnosis. Clinical metagenome next-generation sequencing (mNGS) may have potential for its accurate and timely diagnosis. Case Presentation We retrospectively reviewed the medical records of three HIV-infected patients who presented with M. colombiense pneumonia in Zhejiang Province between January 2019 and December 2020. No specific clinical presentations or radiological manifestations were found in any of the patients. The detection of M. colombiense is 28-55 days earlier using mNGS on bronchoalveolar lavage fluid (BALF) compared to traditional culture methods. A combined treatment of rifabutin, clarithromycin, or azithromycin, and ethambutol did not provide timely relief of symptoms in these three patients. In the early stage of treatment, moxifloxacin and linezolid were used for several weeks. The average course of treatment for all three patients was close to 17 months. Conclusion We recommend early BALF mNGS for fast and accurate diagnosis of M. colombiense pneumonia in HIV-infected patients with low CD4 counts and long duration of symptoms. Further, moxifloxacin and linezolid may be beneficial in the early stage of treatment.
Collapse
Affiliation(s)
- Yongzheng Guo
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Xiaofeng Li
- The Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, Zhejiang, People’s Republic of China
| | - Qianggu Xiao
- The Department of Infectious Diseases, Xiaoshan First People’s Hospital, Hangzhou, Zhejiang, People’s Republic of China
| | - Jie Yang
- The Department of Infectious Diseases, Lishui Municipal Central Hospital, Lishui, Zhejiang, People’s Republic of China
| | - Ran Tao
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Lijun Xu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Biao Zhu
- The Department of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| |
Collapse
|
4
|
Nguyen MVH, Daley CL. Treatment of Mycobacterium avium Complex Pulmonary Disease: When Should I Treat and What Therapy Should I Start? Clin Chest Med 2023; 44:771-783. [PMID: 37890915 DOI: 10.1016/j.ccm.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Treatment of M avium pulmonary disease requires a three-drug, macrolide-based regimen that is administered for 12 months beyond culture conversion. The regimen can be administered 3 days a week in non-cavitary, nodular bronchiectatic disease but should be given daily when cavitary disease is present. For treatment refractory disease, amikacin liposome inhalation suspension is added to the regimen. Parenteral amikacin or streptomycin should be administered in the setting of extensive radiographic involvement or macrolide resistance. Recurrence of disease is common and often due to reinfection. Novel and repurposed agents are being evaluated in clinical trials.
Collapse
Affiliation(s)
- Minh-Vu H Nguyen
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, CO 80206, USA
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, CO 80206, USA.
| |
Collapse
|
5
|
Yuan X, Xie L, Shi Z, Zhou M. Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers. Front Cell Infect Microbiol 2023; 13:1200157. [PMID: 37545858 PMCID: PMC10403237 DOI: 10.3389/fcimb.2023.1200157] [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] [Received: 04/04/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
Background Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis. Methods We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology. Results Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in α diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for β diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples. Conclusions Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.
Collapse
Affiliation(s)
- Xingya Yuan
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Linshen Xie
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Min Zhou
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
6
|
Li Y, Liu C, Ma A, He W, Qiu Q, Zhao Y, Li Y. Identification and drug susceptibility testing of the subspecies of Mycobacterium avium complex clinical isolates in mainland China. J Glob Antimicrob Resist 2022; 31:90-97. [PMID: 35660663 DOI: 10.1016/j.jgar.2022.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 10/25/2021] [Accepted: 05/29/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The Mycobacterium avium complex (MAC), comprising a series of subspecies, has a worldwide distribution, with differences in drug susceptibility among subspecies. This study aimed to assess the composition of MAC and susceptibility differences among subspecies in mainland China. METHODS A total of 287 MAC clinical strains were included in the study. Multitarget sequences were applied to accurately identify subspecies, and a microdilution method was used to evaluate minimum inhibitory concentrations (MICs) among subspecies using Sensititre SLOMYCO plates. RESULTS Mycobacterium intracellular (N = 169), Mycobacterium avium (N = 52), Mycobacterium chimaera (N = 22), Mycobacterium marseillense (N = 25), Mycobacterium colombiense (N = 14), Mycobacterium yongonense (N = 4), Mycobacterium vulneris (N = 3) and Mycobacterium timonense (N = 2) were isolated from MAC. Clarithromycin, amikacin and rifabutin showed lower MIC50 and MIC90 values than other drugs, and the resistance rates of clarithromycin, amikacin, linezolid and moxifloxacin were 6.3%, 10.5%, 51.9% and 46.3%, respectively. The resistance rates of clarithromycin and moxifloxacin in the initial treatment group were significantly lower than those in the retreatment group (4.09% vs. 12.94%; 30.41% vs. 75.29%; P < 0.05). Drug susceptibility differences were observed in clarithromycin and moxifloxacin among the five major subspecies (P < 0.05); however, those statistically significant differences disappeared when MACs were divided into two groups according to previous anti-tuberculosis (anti-TB) treatment history. CONCLUSION This study revealed that MAC, primarily comprising M. intracellulare, was susceptible to clarithromycin, amikacin and rifabutin. Drug susceptibility among subspecies did not exhibit intrinsic differences in our study. Previous anti-TB treatment patients are more resistant to drugs; thus, attention should be given to those patients in the clinic.
Collapse
Affiliation(s)
- Yuanchun Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aijing Ma
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wencong He
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Qiu
- Research Institute of Tuberculosis, Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Yanming Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China; Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
7
|
Lin S, Hua W, Wang S, Zhang Y, Chen X, Liu H, Shao L, Chen J, Zhang W. In vitro assessment of 17 antimicrobial agents against clinical Mycobacterium avium complex isolates. BMC Microbiol 2022; 22:175. [PMID: 35804298 PMCID: PMC9264595 DOI: 10.1186/s12866-022-02582-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Background Recently, Mycobacterium avium complex (MAC) infections have been increasing, especially in immunocompromised and older adults. The rapid increase has triggered a global health concern due to limited therapeutic strategies and adverse effects caused by long-term medication. To provide more evidence for the treatment of MAC, we studied the in vitro inhibitory activities of 17 antimicrobial agents against clinical MAC isolates. Results A total of 111 clinical MAC isolates were enrolled in the study and they were identified as M. intracellulare, M. avium, M. marseillense, M. colombiense, M. yongonense, and two isolates could not be identified at the species level. MAC strains had relatively low (0–21.6%) resistance to clarithromycin, amikacin, bedaquiline, rifabutin, streptomycin, and clofazimine, and the resistant rates to isoniazid, rifampin, linezolid, doxycycline, and ethionamide were very high (72.1–100%). In addition, M. avium had a significantly higher resistance rate than that of M. intracellulare for ethambutol (92.3% vs 40.7%, P < 0.001), amikacin (15.4% vs 1.2%, P = 0.049), and cycloserine (69.2% vs 25.9%, P = 0.004). Conclusions Our results supported the current usage of macrolides, rifabutin, and aminoglycosides in the regimens for MAC infection, and also demonstrated the low resistance rate against new drugs, such as clofazimine, tedizolid, and bedaquiline, suggesting the possible implementation of these drugs in MAC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02582-2.
Collapse
Affiliation(s)
- Siran Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenya Hua
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shiyong Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinchang Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong Liu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Lingyun Shao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| |
Collapse
|
8
|
Mizzi R, Plain KM, Whittington R, Timms VJ. Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. Front Microbiol 2022; 13:892333. [PMID: 35602010 PMCID: PMC9121174 DOI: 10.3389/fmicb.2022.892333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
Collapse
Affiliation(s)
- Rachel Mizzi
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Karren M Plain
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.,Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Richard Whittington
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, NSW, Australia
| |
Collapse
|
9
|
Hamde F, Dinka H, Naimuddin M. In silico analysis of promoter regions to identify regulatory elements in TetR family transcriptional regulatory genes of Mycobacterium colombiense CECT 3035. J Genet Eng Biotechnol 2022; 20:53. [PMID: 35357597 PMCID: PMC8971250 DOI: 10.1186/s43141-022-00331-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 12/18/2022]
Abstract
Background Mycobacterium colombiense is an acid-fast, non-motile, rod-shaped mycobacterium confirmed to cause respiratory disease and disseminated infection in immune-compromised patients, and lymphadenopathy in immune-competent children. It has virulence mechanisms that allow them to adapt, survive, replicate, and produce diseases in the host. To tackle the diseases caused by M. colombiense, understanding of the regulation mechanisms of its genes is important. This paper, therefore, analyzes transcription start sites, promoter regions, motifs, transcription factors, and CpG islands in TetR family transcriptional regulatory (TFTR) genes of M. colombiense CECT 3035 using neural network promoter prediction, MEME, TOMTOM algorithms, and evolutionary analysis with the help of MEGA-X. Results The analysis of 22 protein coding TFTR genes of M. colombiense CECT 3035 showed that 86.36% and 13.64% of the gene sequences had one and two TSSs, respectively. Using MEME, we identified five motifs (MTF1, MTF2, MTF3, MTF4, and MTF5) and MTF1 was revealed as the common promoter motif for 100% TFTR genes of M. colombiense CECT 3035 which may serve as binding site for transcription factors that shared a minimum homology of 95.45%. MTF1 was compared to the registered prokaryotic motifs and found to match with 15 of them. MTF1 serves as the binding site mainly for AraC, LexA, and Bacterial histone-like protein families. Other protein families such as MATP, RR, σ-70 factor, TetR, LytTR, LuxR, and NAP also appear to be the binding candidates for MTF1. These families are known to have functions in virulence mechanisms, metabolism, quorum sensing, cell division, and antibiotic resistance. Furthermore, it was found that TFTR genes of M. colombiense CECT 3035 have many CpG islands with several fragments in their CpG islands. Molecular evolutionary genetic analysis showed close relationship among the genes. Conclusion We believe these findings will provide a better understanding of the regulation of TFTR genes in M. colombiense CECT 3035 involved in vital processes such as cell division, pathogenesis, and drug resistance and are likely to provide insights for drug development important to tackle the diseases caused by this mycobacterium. We believe this is the first report of in silico analyses of the transcriptional regulation of M. colombiense TFTR genes.
Collapse
Affiliation(s)
- Feyissa Hamde
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| | - Hunduma Dinka
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | - Mohammed Naimuddin
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia.
| |
Collapse
|
10
|
Shin MK, Shin SJ. Genetic Involvement of Mycobacterium avium Complex in the Regulation and Manipulation of Innate Immune Functions of Host Cells. Int J Mol Sci 2021; 22:ijms22063011. [PMID: 33809463 PMCID: PMC8000623 DOI: 10.3390/ijms22063011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium complex (MAC), a collection of mycobacterial species representing nontuberculous mycobacteria, are characterized as ubiquitous and opportunistic pathogens. The incidence and prevalence of infectious diseases caused by MAC have been emerging globally due to complications in the treatment of MAC-pulmonary disease (PD) in humans and the lack of understating individual differences in genetic traits and pathogenesis of MAC species or subspecies. Despite genetically close one to another, mycobacteria species belonging to the MAC cause diseases to different host range along with a distinct spectrum of disease. In addition, unlike Mycobacterium tuberculosis, the underlying mechanisms for the pathogenesis of MAC infection from environmental sources of infection to their survival strategies within host cells have not been fully elucidated. In this review, we highlight unique genetic and genotypic differences in MAC species and the virulence factors conferring the ability to MAC for the tactics evading innate immune attacks of host cells based on the recent advances in genetic analysis by exemplifying M. avium subsp. hominissuis, a major representative pathogen causing MAC-PD in humans. Further understanding of the genetic link between host and MAC may contribute to enhance host anti-MAC immunity, but also provide novel therapeutic approaches targeting the pangenesis-associated genes of MAC.
Collapse
Affiliation(s)
- Min-Kyoung Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea;
| | - Sung Jae Shin
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-2-2228-1813
| |
Collapse
|
11
|
Mallick Gupta A, Mandal S. Distribution of sigma factors delineates segregation of virulent and avirulent Mycobacterium. Arch Microbiol 2021; 203:1627-1640. [PMID: 33432378 DOI: 10.1007/s00203-020-02172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/02/2020] [Accepted: 12/27/2020] [Indexed: 11/26/2022]
Abstract
The genus Mycobacterium includes a wide range of species of both slow and rapid growth under major pathogens, opportunists, and saprophytes. The number and combination of sigma factors are extremely diversified among various species of Mycobacterium. The comparative genome analysis illustrates that SigC, SigD, SigG, SigH, SigK and SigI are dominant among the pathogens. Evolutionary analysis using Bayesian inference on 16S rRNA and MLST-based phylogeny using 14 housekeeping genes distinctly differentiate the slow-growing Mycobacterium from fast growers and segregate pathogens from opportunists and saprophytes. Based on the similarity coefficient upon the allotment of sigma factors in mycobacterial species through UPGMA dendrogram analysis, it is apparent that the pathogens are grouped separately following the similar trend observed from the evolutionary approach. Predominance of a set of sigma factors particularly the pathogenic Mycobacterium co-exists with the distribution of six well-known virulence factors of Mycobacterium (PhoP, PcaA, FbpA, Mce1B, KatG and PE_PGRS30). The pathogenicity responsible sigma factors elicit close resemblance with few notable characters of the known virulence factors. Thus the analysis renders that the distribution of sigma factors of different species of Mycobacterium can be a potential tool to predict their pathogenicity index.
Collapse
Affiliation(s)
- Aayatti Mallick Gupta
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
| |
Collapse
|
12
|
Yu X, Jiang W. Mycobacterium colombiense and Mycobacterium avium Complex Causing Severe Pneumonia in a Patient with HIV Identified by a Novel Molecular-Based Method. Infect Drug Resist 2021; 14:11-16. [PMID: 33442272 PMCID: PMC7797356 DOI: 10.2147/idr.s282190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/18/2020] [Indexed: 12/31/2022] Open
Abstract
Non-tuberculous mycobacteria are conditional pathogens that can cause many diseases, among which pulmonary infections are the most common (65–90%). Mycobacterium avium and Mycobacterium abscessus are non-tuberculous mycobacteria most often associated with lung diseases. Mass spectrometry diagnostic techniques were not effective in Mycobacterium avium complex infection. We report a case of Mycobacterium colombiense and Mycobacterium avium complex causing severe pneumonia in an adult with HIV. Our group developed a novel molecular-based method to identify Mycobacterium species. Novel techniques such as molecular cloning which we have described here can make up for the inability of matrix-assisted laser desorption ionization-time of flight mass spectrometry to distinguish the multiple microorganisms present, and may add to the diagnostic toolkit and increase the accuracy and rapidity of diagnosis in the future.
Collapse
Affiliation(s)
- Xiaoling Yu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Wenqian Jiang
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| |
Collapse
|
13
|
Andreani J, Barrassi L, Davoust B, La Scola B. Evidence of an environmental reservoir for emergent Mycobacterium colombiense. New Microbes New Infect 2020; 35:100666. [PMID: 32280480 PMCID: PMC7139152 DOI: 10.1016/j.nmni.2020.100666] [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: 12/28/2019] [Accepted: 03/06/2020] [Indexed: 10/31/2022] Open
Abstract
Mycobacterium colombiense, which belongs to the M. avium complex, is reported to have been isolated from cases of disseminated infection in both immunocompromised and immunocompetent patients. During the isolation of protists from water samples in French Guyana, we co-isolated a flagellated green alga (Polytoma sp.) and a mycobacterium identified as M. colombiense.
Collapse
Affiliation(s)
- J Andreani
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - L Barrassi
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - B Davoust
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - B La Scola
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| |
Collapse
|
14
|
Pena E, Machado D, Viveiros M, Jordão S. A case report of disseminated Mycobacterium colombiense infection in an HIV patient. Int J Mycobacteriol 2020; 8:295-297. [PMID: 31512608 DOI: 10.4103/ijmy.ijmy_100_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mycobacterium colombiense is a newly recognized member of the Mycobacterium avium complex, and only a few cases of infections caused by this pathogen have been reported. We present an imported case of disseminated disease caused by M. colombiense in an HIV patient in early February 2017.
Collapse
Affiliation(s)
- Eduarda Pena
- Infectious Diseases Department, Matosinhos Local Health Unit, Matosinhos, Portugal
| | - Diana Machado
- Unit of Medical Microbiology, Institute of Hygiene and Tropical Medicine of NOVA University of Lisbon, Lisbon, Portugal
| | - Miguel Viveiros
- Unit of Medical Microbiology, Institute of Hygiene and Tropical Medicine of NOVA University of Lisbon, Lisbon, Portugal
| | - Sofia Jordão
- Infectious Diseases Department, Matosinhos Local Health Unit, Matosinhos, Portugal
| |
Collapse
|
15
|
Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology. Microorganisms 2020; 8:microorganisms8010098. [PMID: 31936743 PMCID: PMC7022546 DOI: 10.3390/microorganisms8010098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.
Collapse
|
16
|
Evaluation of Q Gene Mycobacteria: A novel and easy nucleic acid chromatography method for mycobacterial species identification. J Microbiol Methods 2019; 163:105657. [PMID: 31228476 DOI: 10.1016/j.mimet.2019.105657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022]
Abstract
OBJECTIVES A simple, rapid, and new diagnostic test for mycobacteria, named Q Gene Mycobacteria, has been developed. It is based on multiplex PCR using primers harbouring DNA tags combined with a dipstick nucleic acid chromatography method, which does not require the denaturation of PCR products for hybridization and can identify five species of mycobacteria including Mycobacterium tuberculosis complex (MTC), Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium kansasii, and Mycobacterium gordonae. This study aimed to evaluate Q Gene Mycobacteria for the accurate identification of these five species. METHODS A total of 340 mycobacterial strains/isolates were tested, of which 159 were type strains (four MTC and 155 non-tuberculosis mycobacteria (NTM) including four subspecies) and 181 were clinical isolates (18 M. tuberculosis, two Mycobacterium bovis Bacillus Calmette et Guérin (BCG), and 161 NTM comprising 16 species) collected from eight laboratories and hospitals in Japan. Species identification of NTM isolates was performed using the DNA-DNA hybridization method and/or direct sequencing of 16S rRNA, hsp65, and rpoB genes. Q Gene Mycobacteria was compared with above conventional methods for identifying the five species. RESULTS Q Gene Mycobacteria showed excellent concordance for species identification, specifically 99.4% (158/159) for type strains and 99.4% (180/181) for clinical isolates. The two strains that were misidentified as M. gordonae were Mycobacterium paragordonae. As they are genetically close and there is few case reports of M. paragordonae, it might not be a serious critical issue to distinguish M. paragordonae from M. gordonae. CONCLUSIONS Q Gene Mycobacteria was able to identify frequently isolated mycobacterial species accurately and easily. Therefore, Q Gene Mycobacteria could be a useful tool for the identification of specific mycobacteria in clinical laboratories.
Collapse
|
17
|
Zhu J, Liu R, Cao N, Yu J, Liu X, Yu Z. Mycobacterial metabolic characteristics in a water meter biofilm revealed by metagenomics and metatranscriptomics. WATER RESEARCH 2019; 153:315-323. [PMID: 30739073 DOI: 10.1016/j.watres.2019.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/27/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mycobacteria represent one of the most persistent bacterial populations in drinking water distribution system (DWDS) biofilm communities; however, mycobacterial in situ metabolic profiles are largely unknown. In this study, the metabolic characteristics of mycobacteria in a household water meter biofilm were unveiled using a coupled metagenomic/metatranscriptomic approach. The water meter biofilm appeared to express nitrogenase genes (nifDKH) and a full complement of genes coding for several carbon-fixation pathways, especially the Calvin cycle, suggesting the CO2 sequestration and dinitrogen fixation potential of the biofilm. These findings indicate that it may be difficult to prevent the formation of DWDS biofilms simply by controlling the availability of organic carbon or nitrogen. The composite genome of mycobacteria (CG-M) was reconstructed based on the obtained omics data. CG-M shared similar genome phylogeny and virulence-factor profiles with Mycobacterium avium complex, suggesting that population CG-M might represent a member of mycobacteria with pathogenicity. According to the gene expression patterns, population CG-M showed the metabolic potential to assimilate CO2 via the Calvin cycle and/or anaplerotic reactions, and even to grow autotrophically with CO as the sole carbon and energy source. This suggests that organic carbon may not be a limiting factor for mycobacterial growth in DWDSs. Moreover, our results suggest that mycobacterial aromatic degradation is primarily achieved through the catechol meta-cleavage pathway, and biofilm mycobacteria could prefer phosphate as the phosphorus source.
Collapse
Affiliation(s)
- Junge Zhu
- University of Chinese Academy of Sciences, Beijing, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- University of Chinese Academy of Sciences, Beijing, China.
| | - Nan Cao
- Beijing Waterworks Group, Beijing, China
| | - Jianwei Yu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xinchun Liu
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
18
|
Epperson LE, Timke M, Hasan NA, Godo P, Durbin D, Helstrom NK, Shi G, Kostrzewa M, Strong M, Salfinger M. Evaluation of a Novel MALDI Biotyper Algorithm to Distinguish Mycobacterium intracellulare From Mycobacterium chimaera. Front Microbiol 2018; 9:3140. [PMID: 30619208 PMCID: PMC6305299 DOI: 10.3389/fmicb.2018.03140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Accurate and timely mycobacterial species identification is imperative for successful diagnosis, treatment, and management of disease caused by nontuberculous mycobacteria (NTM). The current most widely utilized method for NTM species identification is Sanger sequencing of one or more genomic loci, followed by BLAST sequence analysis. MALDI-TOF MS offers a less expensive and increasingly accurate alternative to sequencing, but the commercially available assays used in clinical mycobacteriology cannot differentiate between Mycobacterium intracellulare and Mycobacterium chimaera, two closely related potentially pathogenic species of NTM that are members of the Mycobacterium avium complex (MAC). Because this differentiation of MAC species is challenging in a diagnostic setting, Bruker has developed an improved spectral interpretation algorithm to differentiate M. chimaera and M. intracellulare based on differential spectral peak signatures. Here, we utilize a set of 185 MAC isolates that have been characterized using rpoB locus sequencing followed by whole genome sequencing in some cases, to test the accuracy of the Bruker subtyper software to identify M. chimaera (n = 49) and M. intracellulare (n = 55). 100% of the M. intracellulare and 82% of the M. chimaera isolates were accurately identified using the MALDI Biotyper algorithm. This subtyper module is available with the MALDI Biotyper Compass software and offers a promising mechanism for rapid and inexpensive species determination for M. chimaera and M. intracellulare.
Collapse
Affiliation(s)
- L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | | | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | - Paul Godo
- Mycobacteriology Laboratory, National Jewish Health, Denver, CO, United States
| | - David Durbin
- Mycobacteriology Laboratory, National Jewish Health, Denver, CO, United States
| | - Niels K. Helstrom
- Mycobacteriology Laboratory, National Jewish Health, Denver, CO, United States
| | - Gongyi Shi
- Bruker Daltonics, Billerica, MA, United States
| | | | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States
| | - Max Salfinger
- Mycobacteriology Laboratory, National Jewish Health, Denver, CO, United States
- Department of Medicine, National Jewish Health, Denver, CO, United States
- College of Public Health, University of South Florida, Tampa, FL, United States
| |
Collapse
|
19
|
van Ingen J, Turenne CY, Tortoli E, Wallace RJ, Brown-Elliott BA. A definition of the Mycobacterium avium complex for taxonomical and clinical purposes, a review. Int J Syst Evol Microbiol 2018; 68:3666-3677. [PMID: 30231956 DOI: 10.1099/ijsem.0.003026] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nontuberculous mycobacteria, particularly the Mycobacterium avium complex (MAC) bacteria, are increasingly recognized as opportunistic pathogens of humans. As a result, studies on antibiotic treatment and taxonomy of the MAC are intensifying, but an updated definition of what constitutes the MAC, either for taxonomical studies or for clinical purposes, is lacking. On the basis of literature review and phylogenetic analyses, we propose to define the MAC as a grouping of slow-growing mycobacteria that show corresponding values in at least two of the following targets against either M. avium ATCC 25291T or Mycobacterium intracellulare ATCC 13950T: >99.4 % sequence identity for the full 16S rRNA gene, >98.7 % for the partial (5') 16S rRNA gene, >97.3 % for hsp65 and >94.4 % for rpoB region V. A >97.5 % value in concatenated analyses of >2500 bp that includes 16S rRNA, hsp65 and rpoB gene sequence data or ≥85 % average nucleotide identity to M. avium ATCC 25291T or M. intracellulare ATCC 13950T on basis of whole genome sequencing data is recommended. This molecular definition is based on the distances observed between the classical members of the MAC, M. avium and M. intracellulare. Applying this definition, the complex currently consists of 12 validly published species: Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium arosiense, Mycobacterium vulneris, Mycobacterium bouchedurhonense, Mycobacterium timonense, Mycobacterium marseillense, Mycobacterium yongonense, Mycobacterium paraintracellulare and Mycobacterium lepraemurium.
Collapse
Affiliation(s)
- Jakko van Ingen
- 1Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Enrico Tortoli
- 3Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Richard J Wallace
- 4Mycobacteria/Nocardia Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Barbara A Brown-Elliott
- 4Mycobacteria/Nocardia Laboratory, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| |
Collapse
|
20
|
Draft Genome Sequences of Mycolicibacter senuensis Isolate GF74 and Mycobacterium colombiense Isolates GF28 and GF76 from a Swine Farm in Japan. Microbiol Resour Announc 2018; 7:MRA00936-18. [PMID: 30533627 PMCID: PMC6256605 DOI: 10.1128/mra.00936-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/14/2018] [Indexed: 12/13/2022] Open
Abstract
Several nontuberculous mycobacteria (NTM) occasionally infect humans and animals. Here, we report the draft genome sequences of Mycolicibacter senuensis isolate GF74 (4,792,997 bp) and Mycobacterium colombiense isolates GF28 and GF76 (5,473,554 bp and 5,426,852 bp, respectively) isolated from a swine farm in Japan. Several nontuberculous mycobacteria (NTM) occasionally infect humans and animals. Here, we report the draft genome sequences of Mycolicibacter senuensis isolate GF74 (4,792,997 bp) and Mycobacterium colombiense isolates GF28 and GF76 (5,473,554 bp and 5,426,852 bp, respectively) isolated from a swine farm in Japan. These sequences provide further information on NTM research.
Collapse
|
21
|
Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 404] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
Collapse
Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
22
|
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] [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.
Collapse
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.
| |
Collapse
|
23
|
Gosal J, Lee BC. A case report of fatal disseminated Mycobacterium colombiense infection in a renal transplant recipient. Transpl Infect Dis 2018; 20:e12890. [PMID: 29569810 DOI: 10.1111/tid.12890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/06/2018] [Accepted: 02/14/2018] [Indexed: 11/30/2022]
Abstract
We report the first case of disseminated Mycobacterium colombiense infection in a solid organ transplant recipient. Co-infection with Cryptococcus neoformans led to fatal multisystem organ failure. We review the pathogen and host factors contributing to these opportunistic infections.
Collapse
Affiliation(s)
- Jasmine Gosal
- Division of Medical Microbiology, Department of Pathology, Ottawa Hospital General Campus, University of Ottawa, Ottawa, ON, Canada
| | - B Craig Lee
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Ottawa Hospital General Campus, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
24
|
Lecorche E, Haenn S, Mougari F, Kumanski S, Veziris N, Benmansour H, Raskine L, Moulin L, Cambau E, Aubry A, Brossier F, Chauffour A, Jaffre J, Jarlier V, Robert J, Sougakoff W. Comparison of methods available for identification of Mycobacterium chimaera. Clin Microbiol Infect 2018; 24:409-413. [DOI: 10.1016/j.cmi.2017.07.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
|
25
|
Identification of Mycobacterium species and Rhodococcus equi in peccary lymph nodes. Trop Anim Health Prod 2018; 50:1319-1326. [PMID: 29546549 DOI: 10.1007/s11250-018-1562-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/01/2018] [Indexed: 01/07/2023]
Abstract
Mycobacterium species and the virulence-associated proteins (vapA, vapB, and vapN genes) of Rhodococcus equi isolated from 330 lymph nodes of collared peccaries (Tayassu tajacu) and white-lipped peccaries (Tayassu pecari) intended for human consumption were investigated. Thirty-six (10.9%) R. equi strains were isolated; 3.3% (n = 11/330) were from white-lipped peccary lymph nodes, and 7.6% (25/330) were from collared peccary lymph nodes. Among the 11 isolates of R. equi from the white-lipped peccaries, 90.9% (n = 10/11) were obtained from the mesenteric lymph nodes, and only 9.1% (n = 1/10) were obtained from the mediastinal lymph nodes. In the 25 isolates of R. equi obtained from the collared peccaries, 40.0% (n = 10/25) were recovered from the mesenteric lymph nodes, 36% (n = 9/25) from the submandibular lymph nodes, and 24.0% (n = 6/25) from the mediastinal lymph nodes. No vapA, vapB, or vapN genes (plasmidless) or three host-associated types (pVAPA, pVAPB, and pVAPN) were identified among the R. equi isolates. Mycobacterium species were isolated in 3.03% (n = 10/330) of all the lymph nodes analyzed. Among the 10 mycobacterial isolates, 60% (n = 6/10) were from the white-lipped peccary lymph nodes, and 40% (n = 4/10) were from the collared peccary lymph nodes. Ten Mycobacterium species were detected by PCR-PRA with a predominance of M. avium type 1. Sequencing of the hsp65 and rpob genes revealed mycobacteria that were saprophytic (M. sinense and M. kumamotonense) and potentially pathogenic (M. colombiense and M. intracellulare) to humans and animals. To our knowledge, this is the first description of R. equi and/or mycobacterial species identified in the lymph nodes of peccary specimens. R. equi (plasmidless) and the mycobacterial species described here have been reported as causes of pulmonary and extrapulmonary infections in both immunocompetent and immunocompromised humans.
Collapse
|
26
|
Inagaki Y, Ito T, Kato T, Ono Y, Sawa M. Disseminated Cutaneous Infection of Mycobacterium colombiense in a Patient with Myelodysplastic Syndrome. Intern Med 2018; 57:423-427. [PMID: 29093379 PMCID: PMC5827328 DOI: 10.2169/internalmedicine.7890-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium colombiense (M. colombiense) is a member of the Mycobacterium avium complex (MAC). To our knowledge, this is the third case report of an M. colombiense infection. An 80-year-old man, immunocompromised by myelodysplastic syndrome (MDS), developed a skin rash with exfoliation and eruption on his face and scalp. Mycobacteria were detected in pus samples. Broad-range polymerase chain reaction (PCR) revealed the mycobacteria to be M. colombiense. The lesions resolved after daily administration of rifampicin, ethambutol, and clarithromycin. In conclusion, broad-range PCR identified this rare mycobacterium, allowing for the administration of appropriate combination antibiotic therapy.
Collapse
Affiliation(s)
- Yuichiro Inagaki
- Department of Hematology and Oncology, Anjo Kosei Hospital, Japan
| | - Tatsuya Ito
- Department of Hematology and Oncology, Anjo Kosei Hospital, Japan
- Department of Internal Medicine, Narita Hospital, Japan
| | - Tomonori Kato
- Department of Hematology and Oncology, Anjo Kosei Hospital, Japan
| | - Yoshitaka Ono
- Department of Hematology and Oncology, Anjo Kosei Hospital, Japan
| | - Masashi Sawa
- Department of Hematology and Oncology, Anjo Kosei Hospital, Japan
| |
Collapse
|
27
|
Lee MR, Chien JY, Huang YT, Liao CH, Shu CC, Yu CJ, Hsueh PR. Clinical features of patients with bacteraemia caused by Mycobacterium avium complex species and antimicrobial susceptibility of the isolates at a medical centre in Taiwan, 2008–2014. Int J Antimicrob Agents 2017; 50:35-40. [DOI: 10.1016/j.ijantimicag.2017.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 10/19/2022]
|
28
|
Kim SY, Shin SH, Moon SM, Yang B, Kim H, Kwon OJ, Huh HJ, Ki CS, Lee NY, Shin SJ, Koh WJ. Distribution and clinical significance of Mycobacterium avium complex species isolated from respiratory specimens. Diagn Microbiol Infect Dis 2017; 88:125-137. [DOI: 10.1016/j.diagmicrobio.2017.02.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/15/2022]
|
29
|
Draft Genome Sequence of Mycobacterium colombiense. GENOME ANNOUNCEMENTS 2017; 5:5/14/e00119-17. [PMID: 28385843 PMCID: PMC5383891 DOI: 10.1128/genomea.00119-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mycobacterium colombiense is a rapidly growing mycobacterium initially isolated from the blood of an HIV-positive patient in Colombia. Its 5,854,893-bp draft genome exhibits a G+C content of 67.64%, 5,233 protein-coding genes, and 54 predicted RNA genes.
Collapse
|
30
|
Gonzalez-Perez M, Murcia M, Parra-Lopez C, Blom J, Tauch A. Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense. New Microbes New Infect 2016; 14:98-105. [PMID: 27818776 PMCID: PMC5072152 DOI: 10.1016/j.nmni.2016.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium avium complex (MAC) contains clinically important nontuberculous mycobacteria worldwide and is the second largest medical complex in the Mycobacterium genus after the Mycobacterium tuberculosis complex. MAC comprises several species that are closely phylogenetically related but diverse regarding their host preference, course of disease, virulence and immune response. In this study we provided immunologic and virulence-related insights into the M. colombiense genome as a model of an opportunistic pathogen in the MAC. By using bioinformatic tools we found that M. colombiense has deletions in the genes involved in p-HBA/PDIM/PGL, PLC, SL-1 and HspX production, and loss of the ESX-1 locus. This information not only sheds light on our understanding the virulence mechanisms used by opportunistic MAC pathogens but also has great potential for the designing of species-specific diagnostic tools.
Collapse
Affiliation(s)
- M.N. Gonzalez-Perez
- Microbiology Department, School of Medicine, National University of Colombia, Bogotá, Colombia
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Corresponding author: M. N. Gonzalez-Perez, Microbiology Department, School of Medicine, National University of Colombia, Bogotá, ColombiaMicrobiology DepartmentSchool of MedicineNational University of ColombiaBogotáColombia
| | - M.I. Murcia
- Microbiology Department, School of Medicine, National University of Colombia, Bogotá, Colombia
| | - C. Parra-Lopez
- Microbiology Department, School of Medicine, National University of Colombia, Bogotá, Colombia
| | - J. Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - A. Tauch
- Microbiology Department, School of Medicine, National University of Colombia, Bogotá, Colombia
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| |
Collapse
|
31
|
Adachi T, Ichikawa K, Inagaki T, Moriyama M, Nakagawa T, Ogawa K, Hasegawa Y, Yagi T. Molecular typing and genetic characterization of Mycobacterium avium subsp. hominissuis isolates from humans and swine in Japan. J Med Microbiol 2016; 65:1289-1295. [PMID: 27624954 DOI: 10.1099/jmm.0.000351] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) causes disease in both humans and swine; however, the genetic variations in MAH isolates are unclear. The aim of this study was to elucidate the genetic variations in MAH isolates from humans and swine in Japan. We analysed the 16S-23S rDNA internal transcribed spacer (ITS) sequence and variable number of tandem repeats (VNTRs) using the Mycobacterium avium tandem repeat loci, prevalence of ISMav6 and clarithromycin resistance for MAH isolates from patients with pulmonary MAC (pMAC) disease (n=69), and HIV-seropositive and blood culture-positive (HIV-MAC) patients (n=28) and swine (n=23). In the minimum spanning tree based on VNTR analysis, swine MAC isolates belonged to a cluster distinguishable from that of human pMAC isolates. Isolates from HIV-MAC were scattered throughout both clusters. The three major distinct sequevars, Mav-A, Mav-B and Mav-F, were determined according to 16S-23S rDNA ITS sequence analysis in addition to three new sequevars, Mav-Q, Mav-R and Mav-S. Mav-A and Mav-F comprised the majority of human pMAC strains; in contrast, Mav-B predominated in swine isolates. Distribution of ITS sequevars in the minimum spanning tree based on VNTR analysis showed similar clusters of isolates from different origins, i.e. human pMAC, HIV-MAC and swine. These results, together with ISMav6 possession and clarithromycin resistance, revealed the genetic diversity of MAH strains recovered from humans and swine. Molecular epidemiology and genetic characterization in the present study showed the distinctive genetic evolutionary lineage of MAH strains isolated from human pMAC diseases and swine.
Collapse
Affiliation(s)
- Takashi Adachi
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Kazuya Ichikawa
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Takayuki Inagaki
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Makoto Moriyama
- Department of Pharmacy, National Hospital Organization, Toyohashi Medical Center, Toyohashi 440-8510, Japan
| | - Taku Nakagawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan
| | - Kenji Ogawa
- Department of Pulmonary Medicine, National Hospital Organization, Higashinagoya National Hospital, 5-101 Umemorizaka, Meito-ku, Nagoya, Aichi 468-8620, Japan
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8560, Japan
| |
Collapse
|
32
|
Avian Mycobacteriosis: Still Existing Threat to Humans. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4387461. [PMID: 27556033 PMCID: PMC4983314 DOI: 10.1155/2016/4387461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/31/2016] [Accepted: 06/19/2016] [Indexed: 12/26/2022]
Abstract
The nontuberculous mycobacteria are typically environmental organisms residing in soil and water. These microorganisms can cause a wide range of clinical diseases; pulmonary disease is most frequent, followed by lymphadenitis in children, skin and soft tissue disease, and rare extra pulmonary or disseminated infections. Mycobacterium avium complex is the second most common cause of pulmonary mycobacterioses after M. tuberculosis. This review covers the clinical and laboratory diagnosis of infection caused by the members of this complex and particularities for the treatment of different disease types and patient populations.
Collapse
|
33
|
A fatal case of pulmonary infection by Mycobacterium colombiense in Para State, Amazon Region, Brazil. Diagn Microbiol Infect Dis 2016; 85:344-346. [DOI: 10.1016/j.diagmicrobio.2016.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/02/2016] [Accepted: 02/07/2016] [Indexed: 11/22/2022]
|
34
|
Chenge J, Kavanagh ME, Driscoll MD, McLean KJ, Young DB, Cortes T, Matak-Vinkovic D, Levy CW, Rigby SEJ, Leys D, Abell C, Munro AW. Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis. Sci Rep 2016; 6:26628. [PMID: 27225995 PMCID: PMC4880925 DOI: 10.1038/srep26628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/25/2016] [Indexed: 12/03/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis (TB). The virulent Mtb H37Rv strain encodes 20 cytochrome P450 (CYP) enzymes, many of which are implicated in Mtb survival and pathogenicity in the human host. Bioinformatics analysis revealed that CYP144A1 is retained exclusively within the Mycobacterium genus, particularly in species causing human and animal disease. Transcriptomic annotation revealed two possible CYP144A1 start codons, leading to expression of (i) a “full-length” 434 amino acid version (CYP144A1-FLV) and (ii) a “truncated” 404 amino acid version (CYP144A1-TRV). Computational analysis predicted that the extended N-terminal region of CYP144A1-FLV is largely unstructured. CYP144A1 FLV and TRV forms were purified in heme-bound states. Mass spectrometry confirmed production of intact, His6-tagged forms of CYP144A1-FLV and -TRV, with EPR demonstrating cysteine thiolate coordination of heme iron in both cases. Hydrodynamic analysis indicated that both CYP144A1 forms are monomeric. CYP144A1-TRV was crystallized and the first structure of a CYP144 family P450 protein determined. CYP144A1-TRV has an open structure primed for substrate binding, with a large active site cavity. Our data provide the first evidence that Mtb produces two different forms of CYP144A1 from alternative transcripts, with CYP144A1-TRV generated from a leaderless transcript lacking a 5′-untranslated region and Shine-Dalgarno ribosome binding site.
Collapse
Affiliation(s)
- Jude Chenge
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Madeline E Kavanagh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Max D Driscoll
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Kirsty J McLean
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Douglas B Young
- Centre for Molecular Microbiology and Infection, Imperial College London, London, United Kingdom
| | - Teresa Cortes
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Dijana Matak-Vinkovic
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Colin W Levy
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew W Munro
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom
| |
Collapse
|
35
|
Lee SY, Kim BJ, Kim H, Won YS, Jeon CO, Jeong J, Lee SH, Lim JH, Lee SH, Kim CK, Kook YH, Kim BJ. Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare. Int J Syst Evol Microbiol 2016; 66:3132-3141. [PMID: 27189351 DOI: 10.1099/ijsem.0.001158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three mycobacterial strains, isolated from independent Korean patients with pulmonary infections, belonging to the Mycobacterium intracellulare genotype 1 (INT-1) were characterized using a polyphasic approach. The sequences of the 16S rRNA gene and internal transcribed spacer 1 (ITS1) of the INT-1 strains were identical to those of Mycobacterium intracellulare ATCC 13950T. However, multilocus sequence typing (MLST) analysis targeting five housekeeping genes (hsp65, rpoB, argG, gnd and pgm) revealed the phylogenetic separation of these strains from M. intracellulare ATCC 13950T. DNA-DNA hybridization values of >70 % confirmed that the three isolates belong to the same species, while the values of <70 % between one of them and the type strains of M. intracellulare and Mycobacterium chimaera confirmed their belonging to a distinct species. In addition, phenotypic characteristics such as positive growth on MacConkey agar and in acidic broth culture, unique matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS profiles of lipids, and unique mycolic acids profiles further supported the taxonomic status of these strains as representatives of a novel species of the Mycobacterium avium complex named Mycobacterium paraintracellulare. The type strain is MOTT64T (=KCTC 29084T=JCM 30622T).
Collapse
Affiliation(s)
- So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hong Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yu-Seop Won
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Che Ok Jeon
- School of Biological Sciences, Chung-Ang University, Seoul, Republic of Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Seon Ho Lee
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Ji-Hun Lim
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Seung-Heon Lee
- Korean Institute of Tuberculosis, Chungbuk, Republic of Korea
| | - Chang Ki Kim
- Korean Institute of Tuberculosis, Chungbuk, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Liver Research Institute, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
36
|
Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJ. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis. PLoS One 2016; 11:e0152703. [PMID: 27031100 PMCID: PMC4816341 DOI: 10.1371/journal.pone.0152703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022] Open
Abstract
Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.
Collapse
Affiliation(s)
- Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|
37
|
Identification of ISMyo2, a novel insertion sequence element of IS21 family and its diagnostic potential for detection of Mycobacterium yongonense. BMC Genomics 2015; 16:794. [PMID: 26472562 PMCID: PMC4608216 DOI: 10.1186/s12864-015-1978-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Mycobacterium yongonense, as a novel member of the M. avium complex (MAC), was recently reported to be isolated from human specimens in South Korea and Italy. Due to its close relatedness to other MAC members, particularly M. intracellulare in taxonomic aspects, the development of a novel diagnostic method for its specific detection is necessary for clinical or epidemiologic purposes. Methods Using the Mycobacterium yongonense genome information, we have identified a novel IS-element, ISMyo2. Targeting the ISMyo2 sequence, we developed a real-time PCR method and applied the technique to Mycobacterial genomic DNA. Results To identify proper nucleic acid targets for the diagnosis, comparisons of all insertion sequence (IS) elements of 3 M. intracellulare and 3 M. yongonense strains, whose complete genome sequences we reported recently, led to the selection of a novel target gene, the M. yongonense-specific IS element, ISMyo2 (2,387 bp), belonging to the IS21 family. Next, we developed a real-time PCR method using SYBR green I for M. yongonense-specific detection targeting ISMyo2, producing a 338-bp amplicon. When this assay was applied to 28 Mycobacterium reference strains and 63 MAC clinical isolates, it produced amplicons in only the 6 M. yongonense strains, showing a sensitivity of 100 fg of genomic DNA, suggesting its feasibility as a diagnostic method for M. yongonense strains. Conclusions We identified a novel ISMyo2 IS element belonging to the IS21 family specific to M. yongonense strains via genome analysis, and a real-time PCR method based on its sequences was developed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1978-2) contains supplementary material, which is available to authorized users.
Collapse
|
38
|
Kim SY, Park HY, Jeong BH, Jeon K, Huh HJ, Ki CS, Lee NY, Han SJ, Shin SJ, Koh WJ. Molecular analysis of clinical isolates previously diagnosed as Mycobacterium intracellulare reveals incidental findings of "Mycobacterium indicus pranii" genotypes in human lung infection. BMC Infect Dis 2015; 15:406. [PMID: 26423052 PMCID: PMC4589961 DOI: 10.1186/s12879-015-1140-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 09/22/2015] [Indexed: 11/21/2022] Open
Abstract
Background Mycobacterium intracellulare is a major cause of Mycobacterium avium complex lung disease in many countries. Molecular studies have revealed several new Mycobacteria species that are closely related to M. intracellulare. The aim of this study was to re-identify and characterize clinical isolates from patients previously diagnosed with M. intracellulare lung disease at the molecular level. Methods Mycobacterial isolates from 77 patients, initially diagnosed with M. intracellulare lung disease were re-analyzed by multi-locus sequencing and pattern of insertion sequences. Results Among the 77 isolates, 74 (96 %) isolates were designated as M. intracellulare based on multigene sequence-based analysis. Interestingly, the three remaining strains (4 %) were re-identified as “Mycobacterium indicus pranii” according to distinct molecular phylogenetic positions in rpoB and hsp65 sequence-based typing. In hsp65 sequevar analysis, code 13 was found in the majority of cases and three unreported codes were identified. In 16S–23S rRNA internal transcribed spacer (ITS) sequevar analysis, all isolates of both species were classified within the Min-A ITS sequevar. Interestingly, four of the M. intracellulare isolates harbored IS1311, a M. avium-specific element. Two of three patients infected with “M. indicus pranii” had persistent positive sputum cultures after antibiotic therapy, indicating the clinical relevance of this study. Conclusions This analysis highlights the importance of precise identification of clinical isolates genetically close to Mycobacterium species, and suggests that greater attention should be paid to nontuberculous mycobacteria lung disease caused by “M. indicus pranii”.
Collapse
Affiliation(s)
- Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hye Yun Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Kyeongman Jeon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Seung-Jung Han
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, 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.
| |
Collapse
|
39
|
Boyle DP, Zembower TR, Reddy S, Qi C. Comparison of Clinical Features, Virulence, and Relapse amongMycobacterium aviumComplex Species. Am J Respir Crit Care Med 2015; 191:1310-7. [DOI: 10.1164/rccm.201501-0067oc] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
40
|
Clinical Relevance of Nontuberculous Mycobacteria Isolated from Sputum in a Gold Mining Workforce in South Africa: An Observational, Clinical Study. BIOMED RESEARCH INTERNATIONAL 2015; 2015:959107. [PMID: 26180817 PMCID: PMC4477445 DOI: 10.1155/2015/959107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 12/02/2022]
Abstract
Background. The clinical relevance of nontuberculous mycobacteria (NTM), detected by liquid more than solid culture in sputum specimens from a South African mining workforce, is uncertain. We aimed to describe the current spectrum and relevance of NTM in this population. Methods. An observational study including individuals with sputum NTM isolates, recruited at workforce tuberculosis screening and routine clinics. Symptom questionnaires were administered at the time of sputum collection and clinical records and chest radiographs reviewed retrospectively. Results. Of 232 individuals included (228 (98%) male, median age 44 years), M. gordonae (60 individuals), M. kansasii (50), and M. avium complex (MAC: 38) were the commonest species. Of 38 MAC isolates, only 2 (5.3%) were from smear-positive sputum specimens and 30/38 grew in liquid but not solid culture. MAC was especially prevalent among symptomatic, HIV-positive individuals. HIV prevalence was high: 57/74 (77%) among those tested. No differences were found in probability of death or medical separation by NTM species. Conclusions. M. gordonae, M. kansasii, and MAC were the commonest NTM among miners with suspected tuberculosis, with most MAC from smear-negative specimens in liquid culture only. HIV testing and identification of key pathogenic NTM in this setting are essential to ensure optimal treatment.
Collapse
|
41
|
Sliding Motility, Biofilm Formation, and Glycopeptidolipid Production in Mycobacterium colombiense Strains. BIOMED RESEARCH INTERNATIONAL 2015; 2015:419549. [PMID: 26180799 PMCID: PMC4477443 DOI: 10.1155/2015/419549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 01/15/2023]
Abstract
Mycobacterium colombiense is a novel member of the Mycobacterium avium complex, which produces respiratory and disseminated infections in immunosuppressed patients. Currently, the morphological and genetic bases underlying the phenotypic features of M. colombiense strains remain unknown. In the present study, we demonstrated that M. colombiense strains displaying smooth morphology show increased biofilm formation on hydrophobic surfaces and sliding on motility plates. Thin-layer chromatography experiments showed that M. colombiense strains displaying smooth colonies produce large amounts of glycolipids with a chromatographic behaviour similar to that of the glycopeptidolipids (GPLs) of M. avium. Conversely, we observed a natural rough variant of M. colombiense (57B strain) lacking pigmentation and exhibiting impaired sliding, biofilm formation, and GPL production. Bioinformatics analyses revealed a gene cluster that is likely involved in GPL biosynthesis in M. colombiense CECT 3035. RT-qPCR experiments showed that motile culture conditions activate the transcription of genes possibly involved in key enzymatic activities of GPL biosynthesis.
Collapse
|
42
|
Lahiri A, Sanchini A, Semmler T, Schäfer H, Lewin A. Identification and comparative analysis of a genomic island in Mycobacterium avium
subsp. hominissuis. FEBS Lett 2014; 588:3906-11. [DOI: 10.1016/j.febslet.2014.08.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/26/2022]
|
43
|
Zurita J, Ortega-Paredes D, Mora M, Espinel N, Parra H, Febres L, Zurita-Salinas C. Characterization of the first report of Mycobacterium timonense infecting an HIV patient in an Ecuadorian hospital. Clin Microbiol Infect 2014; 20:O1113-6. [PMID: 24813256 DOI: 10.1111/1469-0691.12675] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/28/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022]
Abstract
Mycobacterium timonense is a non-tuberculous mycobacteria (NTM) described in southern France in 2009, and to our knowledge, not reported again as a human pathogen in indexed literature. The aim of this work was to characterize the first clinical isolate of M. timonense in Ecuador. Time of growth, biochemical tests, thin layer growth test, PCR-RFLP analysis of the hsp65 gene and MALDI-TOF spectra analysis were not able to identify the species. The species identification was achieved through sequencing of rrs, hsp65 and rpoB genes. The results highlight the necessity to set up a sequencing method to identify emerging NTM in Ecuadorian clinical facilities.
Collapse
Affiliation(s)
- J Zurita
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito, Ecuador; Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
We report the draft genome sequence of Mycobacterium vulneris DSM 45247T strain, an emerging, opportunistic pathogen of the Mycobacterium avium complex. The genome described here is composed of 6,981,439 bp (with a G+C content of 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes.
Collapse
|
45
|
Abstract
In light of the increasing prevalence of Mycobacterium avium pulmonary disease and the challenges of treating patients with M. avium infection, consideration of measures to reduce exposure is warranted. Because M. avium inhabits water and soil, humans are surrounded by that opportunistic pathogen. Because infection has been linked to the presence of M. avium in household plumbing, increasing hot water temperature, reducing aerosol (mist) exposures in bathrooms and showers, and installing filters that prevent the passage of mycobacteria will likely reduce M. avium exposure. Granular activated carbon (charcoal) filters support the growth of M. avium and should be avoided. When gardening, avoid the inhalation of soil dusts by using a mask or wetting the soil because peat-rich potting soils have high numbers of mycobacteria.
Collapse
|
46
|
Rindi L, Garzelli C. Genetic diversity and phylogeny of Mycobacterium avium. INFECTION GENETICS AND EVOLUTION 2013; 21:375-83. [PMID: 24345519 DOI: 10.1016/j.meegid.2013.12.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/02/2013] [Accepted: 12/02/2013] [Indexed: 02/02/2023]
Abstract
Mycobacterium avium, one of the species of the M. avium complex (MAC), includes 4 subspecies, i.e., M. avium subsp. hominissuis (MAH), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS) and M. avium subsp. paratuberculosis (MAP), in turn classified into the S (sheep) and C (cattle) types. These subspecies, although closely related, represent distinct organisms, each endowed with specific pathogenetic and host range characteristics, ranging from environmental opportunistic bacteria that cause infections in swine and immunocompromised patients to pathogens of birds and ruminants. The present review summarizes the basic epidemiological and pathological features of the M. avium subspecies, describes the major genomic events responsible of M. avium subspecies diversity (insertion sequences, sequence variations in specific chromosome loci or genes, deletions, duplications and insertions of large genomic regions) and then reconstructs the phylogenetic relationships among the M. avium subspecies.
Collapse
Affiliation(s)
- Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, I-56127 Pisa, Italy.
| | - Carlo Garzelli
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, I-56127 Pisa, Italy
| |
Collapse
|
47
|
Virulence and immune response induced by Mycobacterium avium complex strains in a model of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice. Infect Immun 2013; 81:4001-12. [PMID: 23959717 DOI: 10.1128/iai.00150-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The genus Mycobacterium comprises more than 150 species, including important pathogens for humans which cause major public health problems. The vast majority of efforts to understand the genus have been addressed in studies with Mycobacterium tuberculosis. The biological differentiation between M. tuberculosis and nontuberculous mycobacteria (NTM) is important because there are distinctions in the sources of infection, treatments, and the course of disease. Likewise, the importance of studying NTM is not only due to its clinical significance but also due to the mechanisms by which some species are pathogenic while others are not. Mycobacterium avium complex (MAC) is the most important group of NTM opportunistic pathogens, since it is the second largest medical complex in the genus after the M. tuberculosis complex. Here, we evaluated the virulence and immune response of M. avium subsp. avium and Mycobacterium colombiense, using experimental models of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice. Mice infected intratracheally with a high dose of MAC strains showed high expression of tumor necrosis factor alpha (TNF-α) and inducible nitric oxide synthase with rapid bacillus elimination and numerous granulomas, but without lung consolidation during late infection in coexistence with high expression of anti-inflammatory cytokines. In contrast, subcutaneous infection showed high production of the proinflammatory cytokines TNF-α and gamma interferon with relatively low production of anti-inflammatory cytokines such as interleukin-10 (IL-10) or IL-4, which efficiently eliminate the bacilli but maintain extensive inflammation and fibrosis. Thus, MAC infection evokes different immune and inflammatory responses depending on the MAC species and affected tissue.
Collapse
|
48
|
Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity. PLoS One 2013; 8:e68648. [PMID: 23874704 PMCID: PMC3715504 DOI: 10.1371/journal.pone.0068648] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/30/2013] [Indexed: 12/30/2022] Open
Abstract
Background Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected.
Collapse
|
49
|
Shared Mycobacterium avium genotypes observed among unlinked clinical and environmental isolates. Appl Environ Microbiol 2013; 79:5601-7. [PMID: 23851084 DOI: 10.1128/aem.01443-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our understanding of the sources of Mycobacterium avium infection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates of M. avium from geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in isolates from apparently unlinked patients in two or more geographic locations. Six of the 12 were also observed in environmental isolates. A subset of these isolates was further analyzed by alternative strain genotyping methods, pulsed-field gel electrophoresis and MIRU-VNTR, which confirmed the existence of geographically dispersed strain genotypes. These results suggest that caution should be exercised in interpreting high-resolution genotypic matches as evidence for an acquisition event.
Collapse
|
50
|
Absence of Mycobacterium intracellulare and presence of Mycobacterium chimaera in household water and biofilm samples of patients in the United States with Mycobacterium avium complex respiratory disease. J Clin Microbiol 2013; 51:1747-52. [PMID: 23536397 DOI: 10.1128/jcm.00186-13] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent studies have shown that respiratory isolates from pulmonary disease patients and household water/biofilm isolates of Mycobacterium avium could be matched by DNA fingerprinting. To determine if this is true for Mycobacterium intracellulare, household water sources for 36 patients with Mycobacterium avium complex (MAC) lung disease were evaluated. MAC household water isolates from three published studies that included 37 additional MAC respiratory disease patients were also evaluated. Species identification was done initially using nonsequencing methods with confirmation by internal transcribed spacer (ITS) and/or partial 16S rRNA gene sequencing. M. intracellulare was identified by nonsequencing methods in 54 respiratory cultures and 41 household water/biofilm samples. By ITS sequencing, 49 (90.7%) respiratory isolates were M. intracellulare and 4 (7.4%) were Mycobacterium chimaera. In contrast, 30 (73%) household water samples were M. chimaera, 8 (20%) were other MAC X species (i.e., isolates positive with a MAC probe but negative with species-specific M. avium and M. intracellulare probes), and 3 (7%) were M. avium; none were M. intracellulare. In comparison, M. avium was recovered from 141 water/biofilm samples. These results indicate that M. intracellulare lung disease in the United States is acquired from environmental sources other than household water. Nonsequencing methods for identification of nontuberculous mycobacteria (including those of the MAC) might fail to distinguish closely related species (such as M. intracellulare and M. chimaera). This is the first report of M. chimaera recovery from household water. The study underscores the importance of taxonomy and distinguishing the many species and subspecies of the MAC.
Collapse
|