1
|
Anh NK, Phat NK, Thu NQ, Tien NTN, Eunsu C, Kim HS, Nguyen DN, Kim DH, Long NP, Oh JY. Discovery of urinary biosignatures for tuberculosis and nontuberculous mycobacteria classification using metabolomics and machine learning. Sci Rep 2024; 14:15312. [PMID: 38961191 PMCID: PMC11222504 DOI: 10.1038/s41598-024-66113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) infection diagnosis remains a challenge due to its overlapping clinical symptoms with tuberculosis (TB), leading to inappropriate treatment. Herein, we employed noninvasive metabolic phenotyping coupled with comprehensive statistical modeling to discover potential biomarkers for the differential diagnosis of NTM infection versus TB. Urine samples from 19 NTM and 35 TB patients were collected, and untargeted metabolomics was performed using rapid liquid chromatography-mass spectrometry. The urine metabolome was analyzed using a combination of univariate and multivariate statistical approaches, incorporating machine learning. Univariate analysis revealed significant alterations in amino acids, especially tryptophan metabolism, in NTM infection compared to TB. Specifically, NTM infection was associated with upregulated levels of methionine but downregulated levels of glutarate, valine, 3-hydroxyanthranilate, and tryptophan. Five machine learning models were used to classify NTM and TB. Notably, the random forest model demonstrated excellent performance [area under the receiver operating characteristic (ROC) curve greater than 0.8] in distinguishing NTM from TB. Six potential biomarkers for NTM infection diagnosis, including methionine, valine, glutarate, 3-hydroxyanthranilate, corticosterone, and indole-3-carboxyaldehyde, were revealed from univariate ROC analysis and machine learning models. Altogether, our study suggested new noninvasive biomarkers and laid a foundation for applying machine learning to NTM differential diagnosis.
Collapse
Affiliation(s)
- Nguyen Ky Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Quang Thu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Tran Nam Tien
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Cho Eunsu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Ho-Sook Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Duc Ninh Nguyen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.
| | - Jee Youn Oh
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, 08308, Republic of Korea.
| |
Collapse
|
2
|
Wang P, Morimoto K, Hasegawa N, Hassan M, Chatterjee A. Nontuberculous mycobacterial pulmonary disease added burden to COPD and bronchiectasis in Japan. ERJ Open Res 2024; 10:00911-2023. [PMID: 38978557 PMCID: PMC11228608 DOI: 10.1183/23120541.00911-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/04/2024] [Indexed: 07/10/2024] Open
Abstract
Background and objective Nontuberculous mycobacterial pulmonary disease (NTM-PD) prevalence in Japan is among the highest worldwide. COPD and bronchiectasis are common comorbidities among patients with NTM-PD, and it is challenging to treat NTM-PD in patients with these conditions. There are limited data on the incremental burden that NTM-PD adds to underlying COPD or bronchiectasis in Japan. Therefore, the objective of this study was to assess the incremental burden associated with NTM-PD in patients with pre-existing COPD and/or bronchiectasis. Methods This nested case-control study was based on JMDC, Inc. claims data (2015-2020). Patients with COPD and/or bronchiectasis with NTM-PD (cases) were age and sex matched 1:3 to patients with COPD and/or bronchiectasis without NTM-PD (controls), resulting in three mutually exclusive patient groups (COPD, bronchiectasis or both; with or without NTM-PD). Incremental burden of NTM-PD was assessed within each group by comparing hospitalisations during the 1-year period after NTM-PD diagnosis (index) between cases and controls with both univariate analysis and multivariate analysis adjusting for pre-index comorbidities. Results Univariate analyses in the three patient groups consistently demonstrated incremental hospitalisation burden in cases versus controls (e.g. COPD group: 20% of 492 cases versus 13% of 1476 controls had all-cause hospitalisations; 11% versus 5% had respiratory-related hospitalisations; and 6% versus 2% had COPD-related hospitalisations). Subsequent multivariate analysis further confirmed the findings. Conclusions The substantial incremental burden of hospitalisation associated with NTM-PD in patients with COPD and/or bronchiectasis highlights the urgent need for appropriate management of NTM-PD in Japan.
Collapse
Affiliation(s)
- Ping Wang
- Insmed Incorporated, Bridgewater, NJ, USA
| | - Kozo Morimoto
- Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | | | | | | |
Collapse
|
3
|
Khan S, Ali Y, Baig KS, Hussain U, Ali Z. From Triumph to Trial: A Case Study of Non-Tuberculous Mycobacterium After Tetralogy of Fallot (TOF) Correction in an Immunocompetent Child. Cureus 2024; 16:e62207. [PMID: 39006735 PMCID: PMC11244717 DOI: 10.7759/cureus.62207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacterium simiae, a slow-growing non-tuberculous mycobacterium (NTM), presents diagnostic challenges due to its resemblance to Mycobacterium tuberculosis and other NTMs. While NTM infections and tuberculosis share clinical and radiological features, their management strategies differ. Accurate differentiation is pivotal, as misdiagnosing NTM infections such as MDR-TB can lead to ineffective treatments. A case involving an 11-year-old female with tetralogy of Fallot (TOF) and a pulmonary M. simiae infection underscores the importance of precise diagnosis. Enhancing diagnostic methods is imperative to prevent mismanagement of NTM infections and ensure appropriate care.
Collapse
Affiliation(s)
- Salman Khan
- Cardiovascular Diseases, Rehman Medical Institute, Peshawar, PAK
| | - Yamna Ali
- Internal Medicine, Hayatabad Medical Complex Peshawar, Peshawar, PAK
| | | | - Ujala Hussain
- Internal Medicine, Khyber Teaching Hospital, Peshawar, PAK
| | - Ziad Ali
- Internal Medicine, Rehman Medical Institute, Peshawar, PAK
| |
Collapse
|
4
|
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
|
5
|
Patnaik N, Dey RJ. Label-Free Citrate-Stabilized Silver Nanoparticles-Based, Highly Sensitive, Cost-Effective, and Rapid Visual Method for the Differential Detection of Mycobacterium tuberculosis and Mycobacterium bovis. ACS Infect Dis 2024; 10:426-435. [PMID: 38112513 DOI: 10.1021/acsinfecdis.3c00390] [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: 12/21/2023]
Abstract
Tuberculosis poses a global health challenge, and it demands improved diagnostics and therapies. Distinguishing between Mycobacterium tuberculosis (M. tb) and Mycobacterium bovis (M. bovis) infections holds critical "One Health" significance due to the zoonotic nature of these infections and inherent resistance of M. bovis to pyrazinamide, a key part of the directly observed treatment, short-course (DOTS) regimen. Furthermore, most of the currently used molecular detection methods fail to distinguish between the two species. To address this, our study presents an innovative molecular-biosensing strategy. We developed a label-free citrate-stabilized silver nanoparticle aggregation assay that offers sensitive, cost-effective, and swift detection. For molecular detection, genomic markers unique to M. tb and M. bovis were targeted using species-specific primers. In addition to amplifying species-specific regions, these primers also aid the detection of characteristic deletions in each of the mycobacterial species. Post polymerase chain reaction (PCR), we compared two highly sensitive visual detection methods with respect to the traditional agarose gel electrophoresis. The paramagnetic bead-based bridging flocculation assay successfully discriminates M. tb from M. bovis with a sensitivity of ∼40 bacilli. The second strategy exploits citrate-stabilized silver nanoparticles, which aggregate in the absence of amplified dsDNA on the addition of sodium chloride (NaCl). This technique enables the precise, sensitive, and differential detection of as few as ∼4 bacilli. Our study hence advances tuberculosis detection, overcoming the challenges of M. tb and M. bovis differentiation and offering a quicker alternative to time-consuming methods.
Collapse
Affiliation(s)
- Naresh Patnaik
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad, Telangana State 500078, India
| | - Ruchi Jain Dey
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad, Telangana State 500078, India
| |
Collapse
|
6
|
Abbew ET, Lorent N, Mesic A, Wachinou AP, Obiri-Yeboah D, Decroo T, Rigouts L, Lynen L. Challenges and knowledge gaps in the management of non-tuberculous mycobacterial pulmonary disease in sub-Saharan African countries with a high tuberculosis burden: a scoping review. BMJ Open 2024; 14:e078818. [PMID: 38238184 PMCID: PMC10806640 DOI: 10.1136/bmjopen-2023-078818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
INTRODUCTION In sub-Saharan African (SSA) countries endemic for tuberculosis (TB), previous TB is a significant risk factor for non-tuberculous mycobacterial pulmonary disease (NTM-PD). The deployment of GeneXpert MTB/RIF in pulmonary TB diagnostic work-up regularly identifies symptomatic patients with a positive smear microscopy but negative GeneXpert, indicative of NTM presence. This scoping review outlines recent evidence for NTM-PD diagnosis and management in SSA. OBJECTIVE The review's objective was to outline the risk factors, available diagnostics, management options and outcomes of NTM-PD in high-burden TB settings in SSA using the population-concept-context framework. DESIGN AND DATA SOURCES We searched existing literature from PubMed, Web of Science, African Journals Online, Google Scholar and grey literature. Studies published between January 2005 and December 2022 were retained. Data were extracted into Rayyan software and Mendeley and summarised using Excel. RESULTS We identified 785 potential articles, of which 105 were included in the full-text review, with 7 papers retained. Included articles used international criteria for diagnosing NTM-PD. Multiple papers were excluded due to non-application of the criteria, suggesting challenging application in the SSA setting. Identified risk factors include previous TB, smoking and mining. Most commonly, chest radiography and not CT was used for the radiological diagnosis of PD, which may miss early changes related to NTM-PD. Molecular methods for NTM species identification were employed in research settings, usually at referral centres, but were unavailable for routine care. Most studies did not report a standardised approach to treatment and they were not offered treatment for the specific disease, marking a lack of guidance in treatment decision-making. When treatment was provided, the outcome was often not reported due to the lack of implementation of standardised outcome definitions. CONCLUSIONS These outlined challenges present a unique opportunity for researchers to undertake further studies in NTM-PD and proffer solutions more applicable to SSA.
Collapse
Affiliation(s)
- Elizabeth Tabitha Abbew
- Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
- Internal Medicine, Cape Coast Teaching Hospital, Cape Coast, Central, Ghana
- Biomedical Sciences, University of Antwerp, Antwerp, Antwerpen, Belgium
| | - Natalie Lorent
- Respiratory Diseases, KU Leuven University Hospitals Leuven, Leuven, Flanders, Belgium
- Chronic Diseases and Metabolism, BREATHE Laboratory, Katholieke Universiteit Leuven, Leuven, Flanders, Belgium
| | - Anita Mesic
- Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | | | - Dorcas Obiri-Yeboah
- Microbiology and Immunology, University of Cape Coast School of Medical Sciences, Cape Coast, Central, Ghana
| | - Tom Decroo
- Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Leen Rigouts
- Biomedical Sciences, University of Antwerp, Antwerp, Antwerpen, Belgium
- Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Lutgarde Lynen
- Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| |
Collapse
|
7
|
Ghielmetti G, Loubser J, Kerr TJ, Stuber T, Thacker T, Martin LC, O'Hare MA, Mhlophe SK, Okunola A, Loxton AG, Warren RM, Moseley MH, Miller MA, Goosen WJ. Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Front Microbiol 2023; 14:1307440. [PMID: 38075895 PMCID: PMC10699144 DOI: 10.3389/fmicb.2023.1307440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.
Collapse
Affiliation(s)
- Giovanni Ghielmetti
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Tyler Thacker
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Lauren C. Martin
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michaela A. O'Hare
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sinegugu K. Mhlophe
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abisola Okunola
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark H. Moseley
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
8
|
Wang P, Marras TK, Hassan M, Chatterjee A. Incremental mortality associated with nontuberculous mycobacterial lung disease among US Medicare beneficiaries with chronic obstructive pulmonary disease. BMC Infect Dis 2023; 23:749. [PMID: 37914999 PMCID: PMC10619258 DOI: 10.1186/s12879-023-08689-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a common comorbidity in patients with nontuberculous mycobacterial lung disease (NTMLD). Both conditions are associated with increased morbidity and mortality, but data are lacking on the additional burden associated with NTMLD among patients with COPD. Thus, the goal of this study was to assess the incremental mortality risk associated with NTMLD among older adults with COPD. METHODS A retrospective cohort study was conducted using the US Medicare claims database (2010-2017). Patients with preexisting COPD and NTMLD (cases) were matched 1:3 by age and sex with patients with COPD without NTMLD (control patients). Patients were followed up until death or data cutoff (December 31, 2017). Incremental risk of mortality was evaluated by comparing the proportions of death, annualized mortality rate, and mortality hazard rate between cases and control patients using both univariate and multivariate analyses adjusting for age, sex, comorbidities, and COPD severity. RESULTS A total of 4,926 cases were matched with 14,778 control patients. In univariate analyses, a higher proportion of cases (vs. control patients) died (41.5% vs. 26.7%; P < 0.0001), unadjusted annual mortality rates were higher among cases (158.5 vs. 86.0 deaths/1000 person-years; P < 0.0001), and time to death was shorter for cases. This increased mortality risk was also reflected in subsequent multivariate analyses. Patients with COPD and NTMLD were more likely to die (odds ratio [95% CI], 1.39 [1.27-1.51]), had higher mortality rates (rate ratio [95% CI], 1.36 [1.28-1.45]), and had higher hazard of death (hazard ratio [95% CI], 1.37 [1.28-1.46]) than control patients. CONCLUSIONS The substantial incremental mortality burden associated with NTMLD in patients with COPD highlights the importance of developing interventions targeting this high-risk group and may indicate an unmet need for timely and appropriate management of NTMLD.
Collapse
Affiliation(s)
- Ping Wang
- Insmed Incorporated, 700 US Highway 202/206, Bridgewater, NJ, 08807, USA.
| | - Theodore K Marras
- Medicine, University of Toronto and Toronto Western Hospital, Toronto, ON, Canada
| | - Mariam Hassan
- Insmed Incorporated, 700 US Highway 202/206, Bridgewater, NJ, 08807, USA
| | - Anjan Chatterjee
- Insmed Incorporated, 700 US Highway 202/206, Bridgewater, NJ, 08807, USA
| |
Collapse
|
9
|
Sundararaman B, Sylvester MD, Kozyreva VK, Berrada ZL, Corbett-Detig RB, Green RE. A hybridization target enrichment approach for pathogen genomics. mBio 2023; 14:e0188923. [PMID: 37830873 PMCID: PMC10653935 DOI: 10.1128/mbio.01889-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen's drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology.
Collapse
Affiliation(s)
- Balaji Sundararaman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Matthew D. Sylvester
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Varvara K. Kozyreva
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Zenda L. Berrada
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| |
Collapse
|
10
|
Park J, Kwak N, Chae JC, Yoon EJ, Jeong SH. A Two-Step Real-Time PCR Method To Identify Mycobacterium tuberculosis Infections and Six Dominant Nontuberculous Mycobacterial Infections from Clinical Specimens. Microbiol Spectr 2023; 11:e0160623. [PMID: 37378523 PMCID: PMC10434164 DOI: 10.1128/spectrum.01606-23] [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: 04/16/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Tuberculosis (TB) is an ongoing threat to public health, and furthermore, the incidence of infections by nontuberculous mycobacteria (NTM), whose symptoms are not distinguishable from TB, is increasing globally, thus indicating a need for accurate diagnostics for patients with suspected mycobacterial infections. Such diagnostic strategies need to include two steps, (i) detecting the mycobacterial infections and, if the case is an NTM infection, (ii) identifying the causative NTM pathogen. To eliminate a false-positive TB diagnosis for a host vaccinated by the bacillus Calmette-Guérin (BCG) strain of Mycobacterium bovis, a new target specific for M. tuberculosis species was selected, together with the species-specific targets for the six dominant NTM species of clinical importance, i.e., M. intracellulare, M. avium, M. kansasii, M. massiliense, M. abscessus, and M. fortuitum. Using sets of primers and probes, a two-step real-time multiplex PCR method was designed. The diagnostic performance was assessed by using a total of 1,772 clinical specimens from patients with suspected TB or NTM infection. A total of 69.4% of M. tuberculosis and 28.8% of NTM infections were positive for the primary step of the real-time PCR corresponding to the culture within 10 weeks, and mycobacterial species of 75.5% of the NTM-positive cases were identified by the secondary step. The two-step method described herein presented promising results and similar diagnostic sensitivity and specificity to commercially available real-time PCR kits for detecting TB and NTM infections. The method also enabled the identification of mycobacterial species in three-quarters of NTM infection cases, thus providing a better treatment strategy. IMPORTANCE Tuberculosis (TB) is an ongoing threat to public health. In addition, infection by nontuberculous mycobacteria (NTM) is a nonnegligible issue for global public health, with increasing incidences. Since the antimicrobial treatment strategy needs to be differed by the causative pathogen, a rapid and accurate diagnostic method is necessary. In this study, we developed a two-step molecular diagnostic method using clinical specimens of TB and NTM infection-suspected patients. The diagnostic power of the new method using the novel target was similar to the widely used TB detection kit, and, among the NTM-positive specimens, three-quarters of the NTM species were able to be identified. This simple and powerful method will be useful as it is, and it could be applied easily to a point-of-care diagnostic apparatus for better application to patients, especially those living in developing countries.
Collapse
Affiliation(s)
- Jungho Park
- Division of Biotechnology, Chongbuk National University, Iksan, South Korea
- BioPark Diagnostics Inc., Seoul, South Korea
| | - Naeun Kwak
- BioPark Diagnostics Inc., Seoul, South Korea
- Department of Biomedical Laboratory Science, College of Software and Digital Healthcare Convergence, Yonsei University MIRAE Campus, Wonju, South Korea
| | - Jong-Chan Chae
- Division of Biotechnology, Chongbuk National University, Iksan, South Korea
| | - Eun-Jeong Yoon
- Division of Antimicrobial Resistance Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheonju, South Korea
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| |
Collapse
|
11
|
Liu CJ, Tsai CC, Kuo LC, Kuo PC, Lee MR, Wang JY, Ko JC, Shih JY, Wang HC, Yu CJ. A deep learning model using chest X-ray for identifying TB and NTM-LD patients: a cross-sectional study. Insights Imaging 2023; 14:67. [PMID: 37060419 PMCID: PMC10105818 DOI: 10.1186/s13244-023-01395-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/19/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Timely differentiating between pulmonary tuberculosis (TB) and nontuberculous mycobacterial lung disease (NTM-LD), which are radiographically similar, is important because infectiousness and treatment differ. This study aimed to evaluate whether artificial intelligence could distinguish between TB or NTM-LD patients by chest X-rays (CXRs) from suspects of mycobacterial lung disease. METHODS A total of 1500 CXRs, including 500 each from patients with pulmonary TB, NTM-LD, and patients with clinical suspicion but negative mycobacterial culture (Imitator) from two hospitals, were retrospectively collected and evaluated in this study. We developed a deep neural network (DNN) and evaluated model performance using the area under the receiver operating characteristic curves (AUC) in both internal and external test sets. Furthermore, we conducted a reader study and tested our model under three scenarios of different mycobacteria prevalence. RESULTS Among the internal and external test sets, the AUCs of our DNN model were 0.83 ± 0.005 and 0.76 ± 0.006 for pulmonary TB, 0.86 ± 0.006 and 0.64 ± 0.017 for NTM-LD, and 0.77 ± 0.007 and 0.74 ± 0.005 for Imitator. The DNN model showed higher performance on the internal test set in classification accuracy (66.5 ± 2.5%) than senior (50.8 ± 3.0%, p < 0.001) and junior pulmonologists (47.5 ± 2.8%, p < 0.001). Among different prevalence scenarios, the DNN model has stable performance in terms of AUC to detect TB and mycobacterial lung disease. CONCLUSION DNN model had satisfactory performance and a higher accuracy than pulmonologists on classifying patients with presumptive mycobacterial lung diseases. DNN model could be a complementary first-line screening tool.
Collapse
Affiliation(s)
- Chia-Jung Liu
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng Che Tsai
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lu-Cheng Kuo
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan
| | - Po-Chih Kuo
- Department of Computer Science, National Tsing Hua University, No. 101, Kuang Fu Rd, Sec.2, Hsinchu, 300044, Taiwan.
| | - Meng-Rui Lee
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan.
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan.
| | - Jann-Yuan Wang
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan
| | - Jen-Chung Ko
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
| | - Jin-Yuan Shih
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan
| | - Hao-Chien Wang
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan
- Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, #7, Zhongshan South Rd., Zhongzheng Dist., Taipei, 100226, Taiwan
| |
Collapse
|
12
|
Echeverria G, Rueda V, Espinoza W, Rosero C, Zumárraga MJ, de Waard JH. First Case Reports of Nontuberculous Mycobacterial (NTM) Lung Disease in Ecuador: Important Lessons to Learn. Pathogens 2023; 12:pathogens12040507. [PMID: 37111393 PMCID: PMC10142742 DOI: 10.3390/pathogens12040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) lung infections are often misdiagnosed as tuberculosis, which can lead to ineffective antibiotic treatments. In this report, we present three cases of NTM lung infections in Ecuador that were initially diagnosed and treated as tuberculosis based on the results of sputum smear microscopy. The patients, all male, included two immunocompetent individuals and one HIV-positive subject. Unfortunately, sputum culture was not initiated until late in the course of the disease and the cause of the lung infection, Mycobacterium avium complex (MAC), was only identified after the patients had either passed away or were lost to follow-up. These cases are the first documented cases of NTM lung infections in the English medical literature from Ecuador. We emphasize the importance of accurate diagnosis of NTM infections by culture and identification to species level. Sputum smear staining alone cannot differentiate between mycobacterial species, which can lead to misidentification and ineffective treatments. Additionally, reporting NTM pulmonary disease as a notifiable disease to national TB control programs is recommended to obtain accurate prevalence data. These data are critical in determining the importance of this public health problem and the necessary actions needed to address it.
Collapse
Affiliation(s)
- Gustavo Echeverria
- Instituto de Investigación en Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170518, Ecuador
- Programa de Doctorado, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1063ACV, Argentina
- División Investigación y Desarrollo, BioGENA, Quito 170509, Ecuador
| | - Veronica Rueda
- Instituto de Investigación en Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170518, Ecuador
| | - Wilson Espinoza
- Departamento de Tuberculosis, Hospital de Especialidades Eugenio Espejo, Quito 170401, Ecuador
| | - Carlos Rosero
- Departamento de Tuberculosis, Hospital de Especialidades Eugenio Espejo, Quito 170401, Ecuador
| | - Martín J Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular, IABIMO, INTA-CONICET, Buenos Aires C1063ACV, Argentina
| | - Jacobus H de Waard
- Departamento de Tuberculosis, Instituto de Biomedicina "Jacinto Convit", Universidad Central de Venezuela, Caracas 1010, Venezuela
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito 180602, Ecuador
| |
Collapse
|
13
|
Distinguishing nontuberculous mycobacterial lung disease and Mycobacterium tuberculosis lung disease on X-ray images using deep transfer learning. BMC Infect Dis 2023; 23:32. [PMID: 36658559 PMCID: PMC9854086 DOI: 10.1186/s12879-023-07996-5] [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: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacterial lung disease (NTM-LD) and Mycobacterium tuberculosis lung disease (MTB-LD) have similar clinical characteristics. Therefore, NTM-LD is sometimes incorrectly diagnosed with MTB-LD and treated incorrectly. To solve these difficulties, we aimed to distinguish the two diseases in chest X-ray images using deep learning technology, which has been used in various fields recently. METHODS We retrospectively collected chest X-ray images from 3314 patients infected with Mycobacterium tuberculosis (MTB) or nontuberculosis mycobacterium (NTM). After selecting the data according to the diagnostic criteria, various experiments were conducted to create the optimal deep learning model. A performance comparison was performed with the radiologist. Additionally, the model performance was verified using newly collected MTB-LD and NTM-LD patient data. RESULTS Among the implemented deep learning models, the ensemble model combining EfficientNet B4 and ResNet 50 performed the best in the test data. Also, the ensemble model outperformed the radiologist on all evaluation metrics. In addition, the accuracy of the ensemble model was 0.85 for MTB-LD and 0.78 for NTM-LD on an additional validation dataset consisting of newly collected patients. CONCLUSIONS In previous studies, it was known that it was difficult to distinguish between MTB-LD and NTM-LD in chest X-ray images, but we have successfully distinguished the two diseases using deep learning methods. This study has the potential to aid clinical decisions if the two diseases need to be differentiated.
Collapse
|
14
|
Zhang YL, Pan ZY, Chen J, Li BX, Duan QH, Li YH, Ruan HL, Gan H. Letter to the Editor: Isolation of Nontuberculous Mycobacteria During Multidrug-Resistant Tuberculosis Treatment: Colonization or Disease? Microb Drug Resist 2022; 28:906-908. [PMID: 35905051 DOI: 10.1089/mdr.2022.0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yan-Lin Zhang
- Department of Pulmonary of Critical Care Medicine, Pulmonary and Critical Care Medicine Ward I, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Zhi-Yun Pan
- Department of Pulmonary of Critical Care Medicine, Pulmonary and Critical Care Medicine Ward I, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Jun Chen
- Department of Clinical Laboratory, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Bao-Xue Li
- Department of Radiology, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Qiong-Hong Duan
- Department of Pulmonary of Critical Care Medicine, Pulmonary and Critical Care Medicine Ward I, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Yue-Hua Li
- Department of Pulmonary of Critical Care Medicine, Pulmonary and Critical Care Medicine Ward I, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Han-Li Ruan
- Department of Pulmonary of Critical Care Medicine, Pulmonary and Critical Care Medicine Ward I, Wuhan Pulmonary Hospital, Wuhan, Hubei, China
| | - Hui Gan
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
15
|
Xu P, Yang K, Yang L, Wang Z, Jin F, Wang Y, Feng J. Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease. Front Microbiol 2022; 13:898195. [PMID: 35847073 PMCID: PMC9283093 DOI: 10.3389/fmicb.2022.898195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5% (29/31), 80.6% (25/31), 48.4% (15/31), and 32.3% (10/31), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative samples from patients with compromised immune states or poor responses to empirical antibiotics.
Collapse
Affiliation(s)
- Peng Xu
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ke Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhongli Wang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, Shandong Second Provincial General Hospital, Jinan, China
| | - Fang Jin
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yubao Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| |
Collapse
|
16
|
Shu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y, Rotcheewaphan S, Lyon CJ, Sha W, Zelazny AM, Hu T. Peptidomic analysis of mycobacterial secreted proteins enables species identification. VIEW 2022. [DOI: 10.1002/viw.20210019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Meena Rajagopal
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Lingpeng Zhan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Xiangxing Kong
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Yifan He
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Suwatchareeporn Rotcheewaphan
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
- Department of Microbiology, Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| |
Collapse
|
17
|
Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
Collapse
Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| |
Collapse
|
18
|
Beuchel A, Robaa D, Negatu DA, Madani A, Alvarez N, Zimmerman MD, Richter A, Mann L, Hoenke S, Csuk R, Dick T, Imming P. Structure-Activity Relationship of Anti- Mycobacterium abscessus Piperidine-4-carboxamides, a New Class of NBTI DNA Gyrase Inhibitors. ACS Med Chem Lett 2022; 13:417-427. [PMID: 35300094 PMCID: PMC8919391 DOI: 10.1021/acsmedchemlett.1c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium abscessus causes difficult-to-cure pulmonary infections. The bacterium is resistant to most anti-infective agents, including first line antituberculosis (anti-TB) drugs. MMV688844 (844) is a piperidine-4-carboxamide (P4C) with bactericidal properties against M. abscessus. We recently identified DNA gyrase as the molecular target of 844. Here, we present in silico docking and genetic evidence suggesting that P4Cs display a similar binding mode to DNA gyrase as gepotidacin. Gepotidacin is a member of the Novel Bacterial Topoisomerase Inhibitors (NBTIs), a new class of nonfluoroquinolone DNA gyrase poisons. Thus, our work suggests that P4Cs present a novel structural subclass of NBTI. We describe structure-activity relationship studies of 844 leading to analogues showing increased antibacterial activity. Selected derivatives were tested for their inhibitory activity against recombinant M. abscessus DNA gyrase. Further optimization of the lead structures led to improved stability in mouse plasma and increased oral bioavailability.
Collapse
Affiliation(s)
- Andreas Beuchel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dina Robaa
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Dereje A Negatu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa 1000, Ethiopia
| | - Abdeldjalil Madani
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Lea Mann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Sophie Hoenke
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - René Csuk
- Institut für Chemie, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey 07110, United States.,Department of Microbiology and Immunology, Georgetown University, Washington, D.C. 20057, United States
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| |
Collapse
|
19
|
Epola Dibamba Ndanga M, Babatundé Pacome Achimi Agbo Abdul J, Ronald Edoa J, Chester Mevyann R, Romeo Adegbite B, Mfoumbi A, Mebiame Biyogho C, Beh Mba R, Mahoumbou J, McCall MBB, Peter Grobusch M, Akim Adegnika A, Sunday Alabi A. Non-tuberculous mycobacteria isolation from presumptive tuberculosis patients in Lambaréné, Gabon. Trop Med Int Health 2022; 27:438-444. [PMID: 35167171 DOI: 10.1111/tmi.13736] [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] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The prevalence of clinical cases of pulmonary non-tuberculous mycobacteria (NTM) is increasing worldwide. The aim of this study was to determine the proportion and the NTM species isolated from presumptive tuberculosis patients in Lambaréné, Gabon. METHOD From January 2018 to December 2020, sputum samples from presumptive TB patients were analysed at the tuberculosis reference laboratory of the Centre de Recherches Médicales de Lambaréné. Two sputum samples were collected per patient, and culture was performed using Bactec MGIT 960. The GenoType Mycobacterium CM/AS was used for NTM isolates confirmation and species differentiation. RESULTS Among 1363 sputum samples analysed, 285 (20.9%) were Auramin acid fast bacilli (AFB) smear-positive. NTM were isolated in 137/1363 (10%) of the samples. The most prevalent NTM species was Mycobacterium intracellulare (n=74; 54%). CONCLUSION These results show the presence of NTM among presumptive TB patients in Gabon, which could potentially complicate TB diagnosis. This presents a new public health challenge, and emphasises the need to consider NTM in planning the prevention and management of tuberculosis control.
Collapse
Affiliation(s)
| | | | | | | | - Bayodé Romeo Adegbite
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Center of Tropical Medicine and Travel Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Arnaut Mfoumbi
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | | | - Romual Beh Mba
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Jocelyn Mahoumbou
- Programme National de Lutte contre la Tuberculose, Libreville, Gabon
| | - Matthew B B McCall
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Martin Peter Grobusch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Center of Tropical Medicine and Travel Medicine, Amsterdam University Medical Centers, University of Amsterdam, The Netherlands.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Programme National de Lutte contre la Tuberculose, Libreville, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany.,German Center for Infection Research, Tübingen, Germany.,Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands.,Fondation pour la Recherche Scientifique, Cotonou, Bénin
| | - Abraham Sunday Alabi
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Health Focus GmbH, Potsdam, Germany
| |
Collapse
|
20
|
Laliwala A, Svechkarev D, Sadykov MR, Endres J, Bayles KW, Mohs AM. Simpler Procedure and Improved Performance for Pathogenic Bacteria Analysis with a Paper-Based Ratiometric Fluorescent Sensor Array. Anal Chem 2022; 94:2615-2624. [PMID: 35073053 PMCID: PMC10091516 DOI: 10.1021/acs.analchem.1c05021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacterial infections are the leading cause of morbidity and mortality in the world, particularly due to a delay in treatment and misidentification of the bacterial species causing the infection. Therefore, rapid and accurate identification of these pathogens has been of prime importance. The conventional diagnostic techniques include microbiological, biochemical, and genetic analyses, which are time-consuming, require large sample volumes, expensive equipment, reagents, and trained personnel. In response, we have now developed a paper-based ratiometric fluorescent sensor array. Environment-sensitive fluorescent dyes (3-hydroxyflavone derivatives) pre-adsorbed on paper microzone plates fabricated using photolithography, upon interaction with bacterial cell envelopes, generate unique fluorescence response patterns. The stability and reproducibility of the sensor array response were thoroughly investigated, and the analysis procedure was refined for optimal performance. Using neural networks for response pattern analysis, the sensor was able to identify 16 bacterial species and recognize their Gram status with an accuracy rate greater than 90%. The paper-based sensor was stable for up to 6 months after fabrication and required 30 times lower dye and sample volumes as compared to the analogous solution-based sensor. Therefore, this approach opens avenues to a state-of-the-art diagnostic tool that can be potentially translated into clinical applications in low-resource environments.
Collapse
Affiliation(s)
- Aayushi Laliwala
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Denis Svechkarev
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| | - Marat R. Sadykov
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
| | - Jennifer Endres
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
| | - Aaron M. Mohs
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6858, United States
| |
Collapse
|
21
|
Clinical Characteristics and Antimicrobial Susceptibility of Mycobacterium intracellulare and Mycobacterium abscessus Pulmonary Diseases: A Retrospective Study. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2642200. [PMID: 35035646 PMCID: PMC8759892 DOI: 10.1155/2022/2642200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022]
Abstract
The incidence of nontuberculous mycobacteria (NTM) diseases is increasing every year. The present study was performed to investigate the clinical characteristics, CT findings, and drug susceptibility test (DST) results of patients diagnosed with M. intracellulare or M. abscessus nontuberculous mycobacterial pulmonary disease (NTMPD). This retrospective study included patients diagnosed with NTMPD due to M. intracellulare or M. abscessus for the first time at Anhui Chest Hospital between 01/2019 and 12/2021. The patients were grouped as M. intracellulare-NTMPD group or M. abscessus-NTMPD group. Clinical features, imaging data and DST data, were collected. Patients with M. intracellulare infection had a higher rate of acid-fast smears (66.1% vs. 45.2%, P=0.032) and a higher rate of cavitation based on pulmonary imaging (49.6% vs. 19.4%, P=0.002) than patients with M. abscessus infection, but both groups had negative TB-RNA and GeneXpert results, with no other characteristics significant differences. The results of DST showed that M. intracellulare had high susceptibility rate to moxifloxacin (95.9%), amikacin (90.1%), clarithromycin (91.7%), and rifabutin (90.1%). M. abscessus had the highest susceptibility rate to amikacin (71.0%) and clarithromycin (71.0%). The clinical features of M. intracellulare pneumopathy and M. abscessus pneumopathy are highly similar. It may be easily misdiagnosed, and therefore, early strain identification is necessary. M. intracellulare has a high susceptibility rate to moxifloxacin, amikacin, clarithromycin, and rifabutin, while M. abscessus has the highest susceptibility rate to amikacin and clarithromycin. This study provides an important clinical basis for improving the management of NTMPD.
Collapse
|
22
|
Huang M, Tan Y, Zhang X, Wang Y, Su B, Xue Z, Wang J, Pang Y. Effect of Mixed Infections with Mycobacterium tuberculosis and Nontuberculous Mycobacteria on Diagnosis of Multidrug-Resistant Tuberculosis: A Retrospective Multicentre Study in China. Infect Drug Resist 2022; 15:157-166. [PMID: 35082503 PMCID: PMC8786360 DOI: 10.2147/idr.s341817] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Correct species identification is essential before initiation of TB treatment, due to substantial drug susceptibility profile differences among mycobacterial species. Given that nontuberculous mycobacteria (NTM) are frequently resistant to first-line anti-tuberculosis drugs, cases with mixed infections with Mycobacterium tuberculosis (MTB) and NTM tend to be diagnosed as multidrug-resistant tuberculosis (MDR-TB) cases. Here we report results of a retrospective multicentre study that was conducted to determine the prevalence of TB-NTM infections in previously diagnosed laboratory-confirmed multidrug-resistant tuberculosis (MDR-TB) patients using phenotypic drug susceptibility testing. The results were then used to identify risk factors associated with susceptibility to mixed infections. Methods From January 2019 through December 2019, we retrospectively collected MDR-TB isolates from three TB specialised hospitals. Species identifications of isolates were performed using the MeltPro Myco assay. Results A total of 837 MDR-TB isolates were analysed, of which 22 isolates (2.6%) were found to contain a mixture of NTM and MTB organisms. Significant differences in prevalence rates of mixed infections across regions were observed, with prevalence rates ranging from 0.0% (0/213) in Beijing to 3.4% (12/353) in Fuzhou to 3.7% (10/271) in Guangzhou. Among the 22 patients with NTM-TB mixed infections, a total of five different mycobacterial species were identified, of which the most prevalent species was Mycobacterium intracellulare. Notably, a history of previous TB episodes correlated with higher mixed infection risk. Conclusion The results reported here demonstrated that mixed infections with MTB and NTM occurred in approximately 3% of suspected MDR-TB patients in China. These findings raise concerns about the accuracy of molecular diagnostics-based species identification tests and draw attention to the possibility that NTM-MTB mixed infections will be misdiagnosed as MDR-TB in high TB burden settings.
Collapse
Affiliation(s)
- Mingxiang Huang
- Department of Clinical Laboratory, Fuzhou Pulmonary Hospital and Fujian Medical University Clinical Teaching Hospital, Fuzhou, People’s Republic of China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, People’s Republic of China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People’s Republic of China
| | - Yufeng Wang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People’s Republic of China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, People’s Republic of China
| | - Zhongtan Xue
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People’s Republic of China
| | - Jingping Wang
- Clinical Department, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People’s Republic of China
- Jingping Wang, Clinical Department, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, No. 9, Beiguan Street, Tongzhou District, Beijing, 101149, People’s Republic of China, Tel/Fax +86-10-8950 9029, Email
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People’s Republic of China
- Correspondence: Yu Pang, Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, No. 9, Beiguan Street, Tongzhou District, Beijing, 101149, People’s Republic of China, Tel/Fax +86-10-8950 9359, Email
| |
Collapse
|
23
|
Bai A, Belda O, Dosanjh A. Pulmonary Nontuberculous Mycobacterial Infection in Infants: A Systematic Review. Pediatric Health Med Ther 2021; 12:551-559. [PMID: 35002357 PMCID: PMC8721029 DOI: 10.2147/phmt.s332434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 01/15/2023] Open
Abstract
Limited information and literature exist examining pulmonary infections caused by nontuberculous mycobacterial specifically in an infant population. The objective of our study was to summarize clinical characteristics and outcomes of infant patients with nontuberculous mycobacterial pulmonary infection via systematic literature review to identify common diagnostic and treatment regimens for this infection in infants. A search of MEDLINE and PubMed databases in October 2019 using MeSH search terms “infant,” “NTM,” “pulmonary,” and “Mycobacterium abscessus” yielded 139 articles. Inclusion criteria were i) English-language studies including cases and case series with ii) established nontuberculous mycobacterial pulmonary infection in iii) a patient population of infants no older than 24 months. Patients with cystic fibrosis and any study which did not contain relevant information such as infection and age were excluded. This yielded data on 37 patients extracted from 28 studies analyzed. The most common strain was Mycobacterium avium complex, isolated in 56.8% of patient diagnoses. Bronchoscopy/thoracoscopy with a subsequent culture were the most common diagnostic techniques, utilized in 64.9% of cases. Drug therapeutic treatment was utilized in 86% of cases, with a median of three drugs administered. Notable limitations of this study are the small sample size and its retrospective nature, which relies on information reported in previous case studies. Although there is limited formal clinician consensus on the treatment of NTM pulmonary infection and how it may differ in an infant population, our findings indicate an informal consensus typically involving diagnostic lung specimen culture and antibiotic therapy.
Collapse
Affiliation(s)
- Alice Bai
- Brown University, Providence, RI, USA
- Correspondence: Alice Bai Brown University, 69 Brown St. Mail# 5288, Providence, RI, 02912, USATel +1 770 843-2062 Email
| | | | - Amrita Dosanjh
- Pediatric Respiratory, Affiliated Staff Member, Department of Pediatrics, Rady Children’s Hospital, San Diego, CA, USA
| |
Collapse
|
24
|
Katoch P, Mittal S, Sood S, Shrivastava R. Identification and in silico characterization of transcription termination/antitermination protein NusA of Mycobacterium fortuitum. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
25
|
Sarro YDS, Butzler MA, Sanogo F, Kodio O, Tolofoudie M, Goumane MS, Baya B, Diabate S, Diallo IB, Daniogo D, Dembele BPP, Camara I, Kumar A, Dembele E, Kone B, Achenbach CJ, Theron G, Ouattara K, Toloba Y, Diarra B, Doumbia S, Taiwo B, Holl JL, Murphy RL, Diallo S, McFall SM, Maiga M. Development and clinical evaluation of a new multiplex PCR assay for a simultaneous diagnosis of tuberculous and nontuberculous mycobacteria. EBioMedicine 2021; 70:103527. [PMID: 34391092 PMCID: PMC8365364 DOI: 10.1016/j.ebiom.2021.103527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The prevalence of non-tuberculous mycobacteria (NTM) has been increasing worldwide in both developed and developing countries. NTM infection is clinically indistinguishable from tuberculosis and therefore poses significant challenges in patient management, especially in patients chronically treated for pulmonary TB. In this study, we evaluated a new highly sensitive Multiplex MTB/NTM assay that can differentiate M. tuberculosis complex (MTBC) from all NTM, including the treatable and most common NTM, M. avium complex (MAC). METHODS We developed and optimized a new open- Multiplex MTB/NTM assay with two gene-targets for MTBC (IS6110/senX3-regX3) and two targets for MAC (IS1311/DT1) with samples spiked with stored strains and testing 20 replicates. Patients with presumptive TB and NTM were enrolled at the Respiratory Disease Department of The University Teaching Hospital of Point G, in Mali. FINDINGS In the development stage, the new assay showed a high analytic performance with 100% detections of MTBC and MAC at only 5 colony forming units (CFUs). Overall, without the treatment failure cases, the Multiplex assay and the Xpert showed a sensitivity, specificity, PPV and NPV of 83·3% [66·4-92·6], 96·6% [88·6-99·0], 92·5% [82·3-96·5] and 92·2% [82·7-96·5] and the Xpert had values of 96·7% [83·3-99·4], 80·0% [68·2-88·1], 70·7 [55·5-82·3] and 97·9% [89·3-99·6], respectively. The Multiplex assay successfully detected all (5/5) the MAC cases. INTERPRETATION Our new Multiplex assay demonstrates better specificity than Xpert for all group studied, in addition to detecting potential NTM cases. The assay could therefore complement the widely used Xpert assay and enhance discrimination of TB and NTM infections. FUNDING This work was supported by the National Institutes of Health (R03AI137674, U54EB027049, D43TW010350 and UM1AI069471) and Northwestern University's Institute for Global Health Catalyzer Fund.
Collapse
Affiliation(s)
- Yeya Dit Sadio Sarro
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Fanta Sanogo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ousmane Kodio
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mohamed Tolofoudie
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mariam S Goumane
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Diabate
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Djakaridja Daniogo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bindongo P P Dembele
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Issiaka Camara
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | | | - Bourahima Kone
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Grant Theron
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Khadidia Ouattara
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yacouba Toloba
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Jane L Holl
- University of Chicago, Chicago, Illinois, USA
| | | | - Souleymane Diallo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Northwestern University, Chicago, Illinois, USA.
| |
Collapse
|
26
|
Zulu M, Monde N, Nkhoma P, Malama S, Munyeme M. Nontuberculous Mycobacteria in Humans, Animals, and Water in Zambia: A Systematic Review. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.679501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental opportunistic pathogens of humans and animals that are emerging with a serious public health impact particularly in individuals with Acquired Immunodeficiency Syndromes. Recent scientific evidence is shifting from NTMs being known as traditional environmental organisms to serious pathogenic organisms in both animals and humans. In humans, factors attributable to this rise have been linked mainly to Human Immunodeficiency Virus and Acquired Immunodeficiency Syndrome pandemic. In recent years there has been an increase in multidrug resistant Tuberculosis in Zambia and it is thought that NTMs could possibly be the cause. This study was therefore formulated to review available information on the prevalence of NTM in humans, animals and the environment, species distribution, zoonotic potential and public health importance in Zambia. This review was conducted in accordance with PRISMA guidelines. A literature search was done in PubMed and Google scholar using predefined search terms such as ‘nontuberculous mycobacteria’, ‘atypical mycobacteria’, ‘mycobacteria other than mycobacterium tuberculosis’ and ‘Zambia’, in combination with Boolean operators (AND, OR). This particular systematic review draws findings based on literature search between 2000 and 2020. Through literature search 243 papers were identified, 23 duplicates were identified and removed and 206 articles were excluded as they did not meet the inclusion criteria. The full text of the remaining 14 articles were considered for this review. The overall prevalence of NTM in humans was 24.39%, in water 21.5%, in animals 16.05% of which the prevalence in cattle was 14.81% and Kafue Lechwe 1.23%. Mycobacterium intracellulare was the most common isolated nontuberculous mycobacteria in humans and cattle while Mycobacterium gordonae was the most common in water, and Mycobacterium stomatepiae sp Nov in Kafue Lechwe. Nontuberculous mycobacteria are an emerging public health threat in Zambia both in humans and animals and this calls for the need for molecular information on the zoonotic transmission of nontuberculous mycobacteria. Increased awareness of nontuberculous mycobacteria diseases among clinicians and laboratory personnel is crucial for patient management and an essential step for facilitating the identification of nontuberculous mycobacteria species in laboratories.
Collapse
|
27
|
Larsen SE, Reese VA, Pecor T, Berube BJ, Cooper SK, Brewer G, Ordway D, Henao-Tamayo M, Podell BK, Baldwin SL, Coler RN. Subunit vaccine protects against a clinical isolate of Mycobacterium avium in wild type and immunocompromised mouse models. Sci Rep 2021; 11:9040. [PMID: 33907221 PMCID: PMC8079704 DOI: 10.1038/s41598-021-88291-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 04/05/2021] [Indexed: 01/19/2023] Open
Abstract
The nontuberculous mycobacteria (NTM) Mycobacterium avium is a clinically significant pathogen that can cause a wide range of maladies, including tuberculosis-like pulmonary disease. An immunocompromised host status, either genetically or acutely acquired, presents a large risk for progressive NTM infections. Due to this quietly emerging health threat, we evaluated the ability of a recombinant fusion protein ID91 combined with GLA-SE [glucopyranosyl lipid adjuvant, a toll like receptor 4 agonist formulated in an oil-in-water stable nano-emulsion] to confer protection in both C57BL/6 (wild type) and Beige (immunocompromised) mouse models. We optimized an aerosol challenge model using a clinical NTM isolate: M. avium 2-151 smt, observed bacterial growth kinetics, colony morphology, drug sensitivity and histopathology, characterized the influx of pulmonary immune cells, and confirmed the immunogenicity of ID91 in both mouse models. To determine prophylactic vaccine efficacy against this M. avium isolate, mice were immunized with either ID91 + GLA-SE or bacillus Calmette-Guérin (BCG). Immunocompromised Beige mice displayed a delayed influx of innate and adaptive immune cells resulting in a sustained and increased bacterial burden in the lungs and spleen compared to C57BL/6 mice. Importantly, both ID91 + GLA-SE and BCG vaccines significantly reduced pulmonary bacterial burden in both mouse strains. This work is a proof-of-concept study of subunit vaccine-induced protection against NTM.
Collapse
Affiliation(s)
- Sasha E. Larsen
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| | - Valerie A. Reese
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| | - Tiffany Pecor
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| | - Bryan J. Berube
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| | - Sarah K. Cooper
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Guy Brewer
- Alternative Behavior Strategies Inc, Salt Lake City, UT USA
| | - Diane Ordway
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Marcela Henao-Tamayo
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Brendan K. Podell
- grid.47894.360000 0004 1936 8083Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Susan L. Baldwin
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| | - Rhea N. Coler
- grid.240741.40000 0000 9026 4165Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA USA
| |
Collapse
|
28
|
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and an important cause of disease. The most common species causing pulmonary disease are members of Mycobacterium avium complex (MAC). MAC pulmonary disease (MAC-PD) can be chronic, debilitating, costly, and associated with a high mortality. However, MAC diagnoses are often delayed due to the nonspecific presentation of MAC-PD and radiological findings that overlap with other pulmonary diseases. Patients with risk factors and who meet the diagnostic criteria—which include clinical, radiological, and microbiologic criteria—should be considered for treatment. Diagnosis requires 2 or more positive sputum cultures or 1 bronchoscopic specimen culture. The recommendation for those who are treated is a 3-drug regimen including macrolide, rifamycin, and ethambutol that is continued for 12 months beyond sputum culture conversion to negative. MAC-PD is difficult to treat, with frequent drug-related side effects and suboptimal treatment outcomes. Refractory and recurrent disease is common, leading to lifelong follow-up of patients. There are limited treatment options for patients with macrolide-resistant or refractory disease. Amikacin liposome inhalation suspension is recommended for treatment-refractory patients whose cultures remain positive after 6 months of guideline-based therapy. Among the research priorities to improve patient outcomes and quality of life are developing new, more rapid diagnostic tests, investigating biomarkers associated with disease progression, and identifying new drugs and routes of administration as well as new, shorter, and better-tolerated regimens.
Collapse
Affiliation(s)
- Charles L Daley
- Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kevin L Winthrop
- Professor of Infectious Diseases, School of Medicine Professor of Public Health, School of Public Health Oregon Health and Science University Portland, OR, USA
| |
Collapse
|
29
|
Sharma M, Malhotra B, Tiwari J, Bhargava S. Profile of Nontuberculous Mycobacteria in Patients Suspected of Tuberculosis and Drug-Resistant Tuberculosis. J Lab Physicians 2020; 12:203-211. [PMID: 33268938 PMCID: PMC7684985 DOI: 10.1055/s-0040-1721160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Objective Infections due to nontuberculous mycobacteria (NTM) is increasing globally and may present as drug-resistant tuberculosis (DRTB). In India, data on NTM prevalence and species diversity is limited. Present study was conducted to detect the prevalence and profile of NTM among patients suspected of DRTB using paraffin slide culture (PSC)and mycobacteria growth indicator tube (MGIT) culture methods for isolation of NTM. Material and Method A total of 2,938 samples suspected of TB/DRTB were cultured on PSC and MGIT960. Species identification of mycobacterial isolate was done by sequencing of 16s ribosomal RNA gene. Result Among 2938 samples, 35 (1.19%) were found positive for NTM by PSC and 9 (0.30%) were found positive by MGIT. The diversity of NTM species was high (13 species). Out of 35 NTM isolates by PSC, maximum 34.29% (12) isolates were found to be Mycobacterium fortuitum , followed by 11.43% (4) Mycobacterium abscessus and Mycobacterium chelonae , and 42.85% (15) were other species viz. 8.57% (3) were Mycobacterium intracellulare and Mycobacterium kansasii , 5.71% (2) were Mycobacterium peregrinum , and 2.85% (1) were Mycobacterium flavescens, Mycobacterium farcinogenes, Mycobacterium moriokanese, Mycobacterium wolinskyi, Mycobacterium simiae, Mycobacterium goodii , and Mycobacterium terrae each. Coinfection of Mycobacterium tuberculosis (MTB) and NTM was found in 60% (21) samples. Conclusion Prevalence of NTM was low among multidrug resistant tuberculosis/TB suspected patients, similar to other studies done in India. PSC was found better than MGIT for the isolation of NTM, though poor separation of NTM and MTB on subculture may have led to false negativity in cases of coinfection. About 13 species were isolated; M. fortuitum was the most common of all. Since coinfection of NTM and TB can also occur, samples of patients suspected of NTM should be cultured on PSC even if positive for MTB.
Collapse
Affiliation(s)
- Megha Sharma
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Bharti Malhotra
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Jitendra Tiwari
- Department of Microbiology, Government Medical College, Bharatpur, Rajasthan, India
| | - Shipra Bhargava
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| |
Collapse
|
30
|
Agizew T, Boyd R, Mathebula U, Mathoma A, Basotli J, Serumola C, Pals S, Finlay A, Lekone P, Rankgoane-Pono G, Tlhakanelo T, Chihota V, Auld AF. Outcomes of HIV-positive patients with non-tuberculous mycobacteria positive culture who received anti-tuberculous treatment in Botswana: Implications of using diagnostic algorithms without non-tuberculous mycobacteria. PLoS One 2020; 15:e0234646. [PMID: 32530972 PMCID: PMC7292360 DOI: 10.1371/journal.pone.0234646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 05/31/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Patients with non-tuberculous mycobacteria (NTM) or Mycobacterium tuberculosis (MTB) pulmonary disease may have similar clinical presentation. The potential for misdiagnosis and inappropriate treatment exists in settings with limited testing capacity for Xpert® MTB/RIF (Xpert), phenotypic culture and NTM speciation. We describe treatment outcomes among people living with HIV (PLHIV) who received anti-tuberculosis treatment and were found to have NTM or MTB positive sputum cultures. METHODS PLHIV attending one of the 22 participating HIV clinics, who screened positive for ≥1 tuberculosis (TB) symptoms (cough, fever, night sweats, or weight loss) were asked to submit sputa for culture and speciation from August 2012 to November 2014. The national intensified TB case finding algorithms were followed: initially symptomatic patients were evaluated by testing sputum samples using a smear (smear-based TB diagnostic algorithm) and, after GeneXpert instruments were installed, by testing with Xpert (Xpert-based TB diagnostic algorithm). Within the study period, TB diagnostic algorithms used for MTB did not include screening, diagnosis, and management of NTM. Despite MTB negative culture, some symptomatic patients, including those with NTM positive culture, received empirical anti-TB treatment at the discretion of treating clinicians. Per the World Health Organization treatment outcomes classification: died, treatment failure or loss-to-follow-up were classified as unfavorable (unsuccessful) outcome; cured and treatment completed were classified as favorable (successful) outcome. Empiric treatment was defined as initiating treatment without or before receiving a test result indicating MTB. We compare treatment outcomes and characteristics among patients with NTM or MTB positive culture who received anti-TB treatment. RESULTS Among 314 PLHIV, who were found co-infected with TB, 146 cases had microbiological evidence; and for 131/146 MTB positive cultures were reported. One-hundred fifty-two of the 314 were clinically diagnosed with TB and treated empirically. Among those empirically treated for TB, 36/152 had culture results positive for NTM, and another 43/152 had culture results positive for MTB, reported after patients received empirical anti-TB treatment. Overall, MTB positive culture results were reported for 174 (131 plus 43) patients. Treatment outcomes were available for 32/36 NTM and 139/174 MTB; unfavorable outcomes were 12.5% and 8.7% for NTM and MTB, respectively, p = 0.514, respectively. For 34/36 tested NTM patients, all Xpert results indicated 'no MTB'. Among patients who initially received empiric anti-TB treatment and ultimately were found to have MTB positive culture, the unfavorable outcome was 11.8% (4/34), compared to 12.5% (4/32) of patients with NTM positive culture, Fisher's exact test p = 1.00. CONCLUSIONS While the higher unfavorable outcome was non statistically significant, the impact of inappropriate treatment among NTM patients should not be overlooked. Our findings suggest that Xpert has the potential to rapidly rule-out NTM and avoid sub-optimal treatment; further research is needed to evaluate such potential.
Collapse
Affiliation(s)
- Tefera Agizew
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
- Department of Family Medicine and Public Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Rosanna Boyd
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
- Division of Tuberculosis Elimination, CDC, Atlanta, Georgia, United States of America
| | - Unami Mathebula
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
| | - Anikie Mathoma
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
| | - Joyce Basotli
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
| | | | - Sherri Pals
- Division of Global HIV/AIDS and Tuberculosis, CDC, Atlanta, Georgia, United States of America
| | - Alyssa Finlay
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
- Division of Tuberculosis Elimination, CDC, Atlanta, Georgia, United States of America
| | - Phenyo Lekone
- U.S. Centers for Disease Control and Prevention (CDC), Gaborone, Botswana
| | - Goabaone Rankgoane-Pono
- Ministry of Health and Wellness, National Tuberculosis Control Programme, Gaborone, Botswana
| | - Thato Tlhakanelo
- Department of Family Medicine and Public Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Violet Chihota
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Aurum Institute, Johannesburg, South Africa
| | - Andrew F. Auld
- Division of Global HIV/AIDS and Tuberculosis, CDC, Atlanta, Georgia, United States of America
| |
Collapse
|
31
|
Christopher PM, Widysanto A. GeneXpert Mycobacterium tuberculosis/rifampicin assay for molecular epidemiology of rifampicin-Resistant Mycobacterium tuberculosis in an Urban Setting of Banten province, Indonesia. Int J Mycobacteriol 2020; 8:351-358. [PMID: 31793505 DOI: 10.4103/ijmy.ijmy_138_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Tuberculosis (TB) is the fourth leading cause of death in Indonesia. In 2017, the World Health Organization (WHO) estimated that only 2% of the TB patients in Indonesia had only been tested with rapid diagnostics at the time of diagnosis, resulting in largely underdetected rifampicin-resistant TB (RR-TB). Utilization of GeneXpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay as a point-of-care molecular assay to detect TB and RR-TB and serving its purpose in accordance with the first pillar of the WHO End-TB Strategy. Objective This study investigated the use of GeneXpert MTB/RIF assay to determine the molecular epidemiology of RR-TB in an urban setting of Indonesia. Methods All molecular epidemiological and microbiological databases were retrospectively examined from GeneXpert MTB/RIF assay results in Siloam Hospital Lippo Village. The sociodemographic characteristics and results of microbiological examinations consisting of Ziehl-Neelsen staining and GeneXpert MTB/RIF assay were analyzed. Results During the study period, 600 cases were registered, and GeneXpert MTB/RIF tests were done in which the tests yielded 597 (99.5%) valid results; 62.0% were male and adult of age category; of whom 29 samples (4.9%) were found to be RR-TB, 186 samples (31.2%) were RIF sensitive, and remainders were negative. Conclusions The results of GeneXpert MTB/RIF to be a fundamental diagnosis of RR-TB and subsequently to notify MDR-TB were satisfying and valuable in this study. This further increased and reinforced TB surveillance and national TB program to finally bring about WHO end-TB strategy one step closer in Indonesia.
Collapse
Affiliation(s)
- Paulus Mario Christopher
- Department of Microbiology, Faculty of Medicine, Pelita Harapan University, Tangerang, Banten, Indonesia
| | -
- Department of Microbiology, Faculty of Medicine, Pelita Harapan University, Tangerang, Banten, Indonesia
| | - Allen Widysanto
- Department of Respirology, Faculty of Medicine, Pelita Harapan University, Tangerang, Banten, Indonesia
| |
Collapse
|
32
|
Luukinen BV, Vuento R, Hirvonen JJ. Evaluation of a semi-automated Seegene PCR workflow with MTB, MDR, and NTM detection for rapid screening of tuberculosis in a low-prevalence setting. APMIS 2020; 128:406-413. [PMID: 32202675 DOI: 10.1111/apm.13040] [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] [Received: 01/22/2020] [Accepted: 03/02/2020] [Indexed: 11/28/2022]
Abstract
In areas of low tuberculosis (TB) prevalence, laboratory diagnosis of TB may essentially cover non-tuberculous mycobacteria (NTM) in addition to Mycobacterium tuberculosis (MTB). In this study, a semi-automated PCR workflow distinguishing MTB and NTM (Anyplex™ MTB/NTMe, Seegene) and subsequently detecting MTB isoniazid/rifampicin resistance (Allplex™ MTB/MDRe, Seegene) was evaluated for replacing smear microscopy of acid-fast bacilli as the rapid screening method for TB. With 279 clinical samples, 47 cultures positive for MTB and 76 for NTM, the Anyplex™ MTB/NTMe assay and smear microscopy showed equal sensitivities (49.6% vs 50.8%, respectively) but Anyplex™ MTB/NTMe was more sensitive for MTB (63.8% vs 25.6%) than for NTM (40.8% vs 64.5%). Allplex™ MTB/MDRe showed a slightly higher sensitivity of 68.1% for MTB (32/47 positive, n = 222). Antibiotic resistance profiles were correctly identified for all MTB isolates (one MDR isolate). Specificity was 100% for both assays. Anyplex™ MTB/NTMe detected all the 18 NTM species present in the study. The analytical performance of the evaluated high-throughput workflow was relatively weak compared to culture but potentially adequate as a rapid screening method analogous to smear microscopy with additional differentiation between TB, MDR-TB, and NTM.
Collapse
Affiliation(s)
- Bruno Vincent Luukinen
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Risto Vuento
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - Jari Juhani Hirvonen
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland.,Mobidiag, Espoo, Finland
| |
Collapse
|
33
|
A pilot study: VereMTB detection kit for rapid detection of multidrug-resistant mycobcterium tuberculosis in clinical sputum samples. PLoS One 2020; 15:e0228312. [PMID: 32150745 PMCID: PMC7062499 DOI: 10.1371/journal.pone.0228312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/31/2019] [Indexed: 11/19/2022] Open
Abstract
The performance of VereMTBTM Detection Kit for detection of multidrug-resistant tuberculosis (MDR-TB) was validated by using 124 sputum samples. Comparing with MGIT culture, the sensitivity and specificity of VereMTB Detection Kit for MTBC detection were 97.0% and 98.3%, respectively. Compared with MGIT DST, the sensitivity and specificity of VereMTB Detection Kit for RIF resistance detection were 85.7% and 93.9%, respectively, and the sensitivity and specificity of VereMTB Detection Kit for INH resistance detection were 75.0% and 95.7%, respectively. 6 NTM samples were also detected and identified correctly. The VereMTB Detection Kit can detect MDR-TB rapidly and accurately in sputum samples from TB suspects.
Collapse
|
34
|
Jain A, Sinha K, Singh P, Singh U, Dixit P. Occurrence and diversity of non-tuberculous mycobacteria among suspected and confirmed cases of pulmonary tuberculosis. ACTA ACUST UNITED AC 2020. [DOI: 10.4103/jacm.jacm_13_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
35
|
Whittaker E, López-Varela E, Broderick C, Seddon JA. Examining the Complex Relationship Between Tuberculosis and Other Infectious Diseases in Children. Front Pediatr 2019; 7:233. [PMID: 31294001 PMCID: PMC6603259 DOI: 10.3389/fped.2019.00233] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Millions of children are exposed to tuberculosis (TB) each year, many of which become infected with Mycobacterium tuberculosis. Most children can immunologically contain or eradicate the organism without pathology developing. However, in a minority, the organism overcomes the immunological constraints, proliferates and causes TB disease. Each year a million children develop TB disease, with a quarter dying. While it is known that young children and those with immunodeficiencies are at increased risk of progression from TB infection to TB disease, our understanding of risk factors for this transition is limited. The most immunologically disruptive process that can happen during childhood is infection with another pathogen and yet the impact of co-infections on TB risk is poorly investigated. Many diseases have overlapping geographical distributions to TB and affect similar patient populations. It is therefore likely that infection with viruses, bacteria, fungi and protozoa may impact on the risk of developing TB disease following exposure and infection, although disentangling correlation and causation is challenging. As vaccinations also disrupt immunological pathways, these may also impact on TB risk. In this article we describe the pediatric immune response to M. tuberculosis and then review the existing evidence of the impact of co-infection with other pathogens, as well as vaccination, on the host response to M. tuberculosis. We focus on the impact of other organisms on the risk of TB disease in children, in particularly evaluating if co-infections drive host immune responses in an age-dependent way. We finally propose priorities for future research in this field. An improved understanding of the impact of co-infections on TB could assist in TB control strategies, vaccine development (for TB vaccines or vaccines for other organisms), TB treatment approaches and TB diagnostics.
Collapse
Affiliation(s)
- Elizabeth Whittaker
- Department of Paediatrics, Imperial College London, London, United Kingdom
- Department of Paediatric Infectious Diseases, Imperial College Healthcare NHS Trust, St. Mary's Campus, London, United Kingdom
| | - Elisa López-Varela
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Claire Broderick
- Department of Paediatrics, Imperial College London, London, United Kingdom
| | - James A. Seddon
- Department of Paediatrics, Imperial College London, London, United Kingdom
- Department of Paediatric Infectious Diseases, Imperial College Healthcare NHS Trust, St. Mary's Campus, London, United Kingdom
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
36
|
Baya B, Achenbach CJ, Kone B, Toloba Y, Dabitao DK, Diarra B, Goita D, Diabaté S, Maiga M, Soumare D, Ouattara K, Kanoute T, Berthe G, Kamia YM, Sarro YDS, Sanogo M, Togo ACG, Dembele BPP, Coulibaly N, Kone A, Akanbi M, Belson M, Dao S, Orsega S, Siddiqui S, Doumbia S, Murphy RL, Diallo S. Clinical risk factors associated with multidrug-resistant tuberculosis (MDR-TB) in Mali. Int J Infect Dis 2019; 81:149-155. [PMID: 30772470 PMCID: PMC6481646 DOI: 10.1016/j.ijid.2019.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/04/2019] [Accepted: 02/08/2019] [Indexed: 11/26/2022] Open
Abstract
Background MDR-TB is a major threat to global TB control. In 2015, 580,000 were treated for MDR-TB worldwide. The worldwide roll-out of GeneXpert MTB/RIF® has improved diagnosis of MDR-TB; however, in many countries laboratories are unable to assess drug resistance and clinical predictors of MDR-TB could help target suspected patients. In this study, we aimed to determine the clinical factors associated with MDR-TB in Bamako, Mali. Methods We performed a cross-sectional study of 214 patients with presumed MDR-TB admitted to University of Bamako Teaching Hospital, Point-G between 2007 and 2016. We calculated crude and adjusted odds ratios for MDR-TB disease diagnosis using SPSS. Results We found that age ≤40years (OR = 2.56. 95% CI: 1.44–4.55), two courses of prior TB treatment (OR = 3.25,95% CI: 1.44–7.30), TB treatment failure (OR = 3.82,95% CI 1.82–7.79), sputum microscopy with 3+ bacilli load (OR = 1.98, 95% CI: 1.13–3.48) and a history of contact with a TB patient (OR = 2.48, 95% CI: 1.11–5.50) were significantly associated with confirmation of MDR-TB disease. HIV was not a risk factor for MDR-TB (aOR = 0.88, 95% CI: 0.34–1.94). Conclusion We identified several risk factors that could be used to identify MDR-TB suspects and prioritize them for laboratory confirmation. Prospective studies are needed to understand factors associated with TB incidence and clinical outcomes of TB treatment and disease.
Collapse
Affiliation(s)
- Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | | | - Bourahima Kone
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Yacouba Toloba
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Djeneba K Dabitao
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Drissa Goita
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Seydou Diabaté
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Mamoudou Maiga
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Northwestern University, Chicago, IL, USA.
| | - Dianguina Soumare
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Khadidia Ouattara
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Tenin Kanoute
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Gaoussou Berthe
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Youssouf M Kamia
- Department of Pneumo-phtisiology, University Teaching Hospital of Point G, Bamako, Mali.
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Antieme C G Togo
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Bindongo P P Dembele
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Nadie Coulibaly
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Amadou Kone
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | | | - Michael Belson
- National Institute of Allergic and Infectious Diseases (NIAID), Rockville, MD, USA.
| | - Sounkalo Dao
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | - Susan Orsega
- National Institute of Allergic and Infectious Diseases (NIAID), Rockville, MD, USA.
| | - Sophia Siddiqui
- National Institute of Allergic and Infectious Diseases (NIAID), Rockville, MD, USA.
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| | | | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.
| |
Collapse
|
37
|
Schiff HF, Jones S, Achaiah A, Pereira A, Stait G, Green B. Clinical relevance of non-tuberculous mycobacteria isolated from respiratory specimens: seven year experience in a UK hospital. Sci Rep 2019; 9:1730. [PMID: 30741969 PMCID: PMC6370870 DOI: 10.1038/s41598-018-37350-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
The frequency of isolation of non-tuberculous mycobacteria (NTM) species from respiratory specimens is increasing, however the clinical relevance of such identifications vary by mycobacterial species and geographical location. A retrospective study of 853 NTM isolates from respiratory samples from 386 patients over seven years was performed. Clinical records and radiographic information were examined. Clinical significance was assessed by American Thoracic Society diagnostic criteria. 25% of all patients with respiratory isolates met criteria for non-tuberculous mycobacterial pulmonary disease (NTM-PD). Significant symptoms were weight loss, fever, night sweats, productive cough and haemoptysis. HIV co-infection was a significant risk factor for disease. Cavities, nodules and tree-in-bud were significant radiographic findings. Mycobacterium avium complex (MAC) were the dominant species isolated from this patient cohort. Mycobacterium abscessus (M. abscessus) was the species most likely to cause clinically significant disease and be sputum smear positive, thus warranting particular attention.
Collapse
Affiliation(s)
- H F Schiff
- Clinical and Experimental Sciences, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK.
| | - S Jones
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - A Achaiah
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - A Pereira
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - G Stait
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| | - B Green
- Department of Respiratory Medicine, Queen Alexandra Hospital, Southwick Hill Road, Cosham, Portsmouth, PO6 3LY, UK
| |
Collapse
|
38
|
Drummond WK, Kasperbauer SH. Nontuberculous Mycobacteria: Epidemiology and the Impact on Pulmonary and Cardiac Disease. Thorac Surg Clin 2019; 29:59-64. [PMID: 30454922 DOI: 10.1016/j.thorsurg.2018.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This article reviews the current epidemiology of nontuberculous mycobacterial pulmonary disease and the impact on thoracic disease. The prevalence of nontuberculous pulmonary disease in the United States is much higher than that of Mycobacterium tuberculosis. Estimates support an annual increase in incidence of 8% per year. Nontuberculous mycobacteria are distinguished by 2 group designations, slowly growing mycobacteria, such as Mycobacterium avium complex, and rapidly growing mycobacteria, which includes Mycobacterium abscessus. Most pulmonary infections in humans are caused by species belonging to M avium complex. This article also reviews risk factors for disease acquisition, including host and environmental risk factors.
Collapse
Affiliation(s)
- Wendi K Drummond
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Shannon H Kasperbauer
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
| |
Collapse
|
39
|
Sarro YDS, Kone B, Diarra B, Kumar A, Kodio O, Fofana DB, Achenbach CJ, Beavogui AH, Seydi M, Holl JL, Taiwo B, Diallo S, Doumbia S, Murphy RL, McFall SM, Maiga M. Simultaneous diagnosis of tuberculous and non-tuberculous mycobacterial diseases: Time for a better patient management. CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2018; 3:10.15761/CMID.1000144. [PMID: 30613797 PMCID: PMC6319944 DOI: 10.15761/cmid.1000144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Tuberculosis (TB) is the deadliest infectious disease in the world which disproportionately affects low-and-middle-income countries (LMICs) where diagnostic resources and treatment options are limited. The incidence of pulmonary non-tuberculous mycobacteria (NTM) disease is also rapidly increasing in these regions traditionally dominated by TB infections. This poses significant diagnostic and treatment challenges, since these two diseases are often indistinguishable clinically or by sputum smear microscopy (SSM), the most commonly used TB diagnostic tool in LMICs. Consequently, NTM-infected patients usually receive unnecessary TB treatment for months. TB patients with NTM co-infections may also be treated incorrectly due to inaccurate SSM and Xpert™ MTB/RIF (M. tuberculosis./rifampin) results. These issues complicate the management of patients and contribute to the worsening of the current TB and NTM epidemiological features including development of drug resistant strains. It is therefore critical to develop improved diagnostic tools to accurately distinguish these two different pathogens that have many similar clinical and epidemiological features but have different treatment regimens. In this review, we will discuss limitations with current diagnostic tools and the need to develop novel techniques that can accurately and simultaneously diagnose TB and NTM disease._.
Collapse
Affiliation(s)
- Yeya DS Sarro
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bourahima Kone
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bassirou Diarra
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Ousmane Kodio
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djeneba B Fofana
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | | | - Jane L Holl
- Northwestern University, Chicago, Illinois, USA
| | | | - Souleymane Diallo
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Seydou Doumbia
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- Northwestern University, Chicago, Illinois, USA
| |
Collapse
|
40
|
Prevalence of Nontuberculous Mycobacteria: A Single Center Study in Tehran, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2018. [DOI: 10.5812/archcid.61042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
41
|
Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
Collapse
Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| |
Collapse
|
42
|
Bonnet M, San KC, Pho Y, Sok C, Dousset JP, Brant W, Hurtado N, Eam KK, Ardizzoni E, Heng S, Godreuil S, Yew WW, Hewison C. Nontuberculous Mycobacteria Infections at a Provincial Reference Hospital, Cambodia. Emerg Infect Dis 2018. [PMID: 28628437 PMCID: PMC5512507 DOI: 10.3201/eid2307.170060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prevalence of nontuberculous mycobacteria (NTM) disease is poorly documented in countries with high prevalence of tuberculosis (TB). We describe prevalence, risk factors, and TB program implications for NTM isolates and disease in Cambodia. A prospective cohort of 1,183 patients with presumptive TB underwent epidemiologic, clinical, radiologic, and microbiologic evaluation, including >12-months of follow-up for patients with NTM isolates. Prevalence of NTM isolates was 10.8% and of disease was 0.9%; 217 (18.3%) patients had TB. Of 197 smear-positive patients, 171 (86.8%) had TB confirmed (167 by culture and 4 by Xpert MTB/RIF assay only) and 11 (5.6%) had NTM isolates. HIV infection and past TB were independently associated with having NTM isolates. Improved detection of NTM isolates in Cambodia might require more systematic use of mycobacterial culture and the use of Xpert MTB/RIF to confirm smear-positive TB cases, especially in patients with HIV infection or a history of TB.
Collapse
|
43
|
Abstract
The global spread of non-tuberculous mycobacteria (NTM) may be due to HIV/AIDS and other environmental factors. The symptoms of NTM and tuberculosis (TB) disease are indistinguishable, but their treatments are different. Lack of research on the epidemiology of NTM infections has led to underestimation of its prevalence within TB endemic countries. This study was designed to determine the prevalence and clinical characteristics of pulmonary NTM in Bamako. A cross-sectional study which include 439 suspected cases of pulmonary TB. From 2006 to 2013 a total of 332 (76%) were confirmed to have sputum culture positive for mycobacteria. The prevalence of NTM infection was 9.3% of our study population and 12.3% of culture positive patients. The seroprevalence of HIV in NTM group was 17.1%. Patients who weighed <55 kg and had TB symptoms other than cough were also significantly more likely to have disease due to NTM as compared to those with TB disease who were significantly more likely to have cough and weigh more than 55 kg (OR 0.05 (CI 0.02–0.13) and OR 0.32 (CI 0.11–0.93) respectively). NTM disease burden in Bamako was substantial and diagnostic algorithms for pulmonary disease in TB endemic countries should consider the impact of NTM.
Collapse
|
44
|
Zhang W, Shu Q, Zhao Z, Fan J, Lyon CJ, Zelazny AM, Hu Y. Antigen 85B peptidomic analysis allows species-specific mycobacterial identification. Clin Proteomics 2018; 15:1. [PMID: 29321721 PMCID: PMC5757288 DOI: 10.1186/s12014-017-9177-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 11/28/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial antigen could identify specific NTM species. METHODS We analyzed predicted tryptic peptides of the major mycobacterial antigen Ag85B for their capacity to distinguish Mycobacterium tuberculosis and three NTM species responsible for the majority of pulmonary infections caused by slow-growing mycobacterial species. Next, we analyzed trypsin-digested culture supernatants of these four mycobacterial species by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to detect candidate species-specific Ag85B peptides, the identity of which were validated by LC-MS/MS performed in parallel reaction monitoring mode. RESULTS Theoretical tryptic digests of the Ag85B proteins of four common mycobacterial species produced peptides with distinct sequences, including two peptides that could each identify the species origin of each Ag85B protein. LC-MS/MS analysis of trypsinized culture supernatants of these four species detected one of these species-specific signature peptides in each sample. Subsequent LC-MS/MS analyses confirmed these results by targeting these species-specific Ag85B peptides. CONCLUSIONS LC-MS/MS analysis of Ag85B peptides from trypsin-digested mycobacterial culture supernatants can rapidly detect and identify common mycobacteria responsible for most pulmonary infections caused by slow-growing mycobacteria, and has the potential to rapidly diagnose pulmonary infections caused by these mycobacteria through direct analysis of clinical specimens.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Respiratory Medicine, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004 Liaoning Province China
| | - Qingbo Shu
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, AZ 85287 USA
| | - Zhen Zhao
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jia Fan
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, AZ 85287 USA
| | - Christopher J. Lyon
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, AZ 85287 USA
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ye Hu
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Arizona State University Biodesign Institute, Tempe, AZ 85287 USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287 USA
| |
Collapse
|
45
|
Agizew T, Basotli J, Alexander H, Boyd R, Letsibogo G, Auld A, Nyirenda S, Tedla Z, Mathoma A, Mathebula U, Pals S, Date A, Finlay A. Higher-than-expected prevalence of non-tuberculous mycobacteria in HIV setting in Botswana: Implications for diagnostic algorithms using Xpert MTB/RIF assay. PLoS One 2017; 12:e0189981. [PMID: 29272273 PMCID: PMC5741233 DOI: 10.1371/journal.pone.0189981] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 12/06/2017] [Indexed: 01/17/2023] Open
Abstract
Background Non-tuberculous mycobacteria (NTM) can cause pulmonary infection and disease especially among people living with HIV (PLHIV). PLHIV with NTM disease may clinically present with one of the four symptoms consistent with tuberculosis (TB). We describe the prevalence of NTM and Mycobacterium tuberculosis complex (MTBC) isolated among PLHIV who presented for HIV care and treatment. Methods All PLHIV patients presenting for HIV care and treatment services at 22 clinical sites in Botswana were offered screening for TB and were recruited. Patients who had ≥1 TB symptom were asked to submit sputa for Xpert MTB/RIF and culture. Culture growth was identified as NTM and MTBC using the SD-Bioline TB Ag MPT64 Kit and Ziehl Neelsen microscopy. NTM and MTBC isolates underwent species identification by the Hain GenoType CM and AS line probe assays. Results Among 16, 259 PLHIV enrolled 3068 screened positive for at least one TB symptom. Of these, 1940 submitted ≥1 sputum specimen, 427 (22%) patients had ≥1 positive-culture result identified phenotypically for mycobacterial growth. Of these 247 and 180 patients were identified as having isolates were NTM and MTBC, respectively. Of the 247 patients identified with isolates containing NTM; 19 were later excluded as not having NTM based on additional genotypic testing. Among the remaining 408 patients 228 (56%, 95% confidence interval, 46–66%) with NTM. M. intracellulare was the most common isolated (47.8%). Other NTMs commonly associated with pulmonary disease included M. malmoense (3.9%), M. avium (2.2%), M. abscessus (0.9%) and M. kansasii (0.4%). After excluding NTM isolates that were non-speciated and M. gordonae 154 (67.5%) of the NTM isolates were potential pathogens. Conclusions In the setting of HIV care and treatment, over-half (56%) of a positive sputum culture among PLHIV with TB symptoms was NTM. Though we were not able to distinguish in our study NTM disease and colonization, the study suggests culture and species identification for PLHIV presenting with TB symptoms remains important to facilitate NTM diagnosis and hasten time to appropriate treatment.
Collapse
Affiliation(s)
- Tefera Agizew
- Centers for Disease Control and Prevention, Gaborone, Botswana
- * E-mail:
| | - Joyce Basotli
- Centers for Disease Control and Prevention, Gaborone, Botswana
| | - Heather Alexander
- Centers for Disease Control and Prevention, Division of Global HIV and TB, Atlanta, Georgia, United States of America
| | - Rosanna Boyd
- Centers for Disease Control and Prevention, Gaborone, Botswana
- Centers for Disease Control and Prevention, Division of Tuberculosis Elimination, Atlanta, Georgia, United States of America
| | - Gaoraelwe Letsibogo
- National Tuberculosis Reference Laboratory, Ministry of Health, Gaborone, Botswana
| | - Andrew Auld
- Centers for Disease Control and Prevention, Division of Global HIV and TB, Atlanta, Georgia, United States of America
| | | | - Zegabriel Tedla
- Centers for Disease Control and Prevention, Gaborone, Botswana
| | - Anikie Mathoma
- Centers for Disease Control and Prevention, Gaborone, Botswana
| | - Unami Mathebula
- Centers for Disease Control and Prevention, Gaborone, Botswana
| | - Sherri Pals
- Centers for Disease Control and Prevention, Division of Global HIV and TB, Atlanta, Georgia, United States of America
| | - Anand Date
- Centers for Disease Control and Prevention, Division of Global HIV and TB, Atlanta, Georgia, United States of America
| | - Alyssa Finlay
- Centers for Disease Control and Prevention, Gaborone, Botswana
- Centers for Disease Control and Prevention, Division of Tuberculosis Elimination, Atlanta, Georgia, United States of America
| |
Collapse
|
46
|
Diarra B, Toloba Y, Konate B, Sanogo M, Togo ACG, Camara F, Berthe G, Soumaré D, Baya B, Goita D, Sarro YDS, Maiga M, Belson M, Orsega S, Dao S, Murphy RL, Siddiqui S, de Jong BC, Doumbia S, Diallo S. Extensively drug resistant tuberculosis in Mali: a case report. BMC Res Notes 2017; 10:561. [PMID: 29110699 PMCID: PMC5674801 DOI: 10.1186/s13104-017-2890-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/31/2017] [Indexed: 11/20/2022] Open
Abstract
Background Drug resistant tuberculosis presents a major public health challenge. Case presentation We present here the first two patients diagnosed with extensively drug resistant tuberculosis in Bamako, Mali. Genotypic findings suggest possible nosocomial transmission from the first patient to the second one, resulting in superinfection of the second patient. After being diagnosed with extensively drug resistant tuberculosis in August 2016, the patients only started receiving appropriate treatment 10 months later. Conclusion The identification of these patients highlights the need for improved diagnostic and treatment algorithms for better surveillance and management of drug resistance in Mali. In the interest of these as well as future patients suffering from resistant tuberculosis, all steps recommended for programmatic management of drug resistant tuberculosis must be urgently prioritized in order to strengthen the multidrug resistant tuberculosis program.
Collapse
Affiliation(s)
- Bassirou Diarra
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali. .,Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Yacouba Toloba
- Service de Pneumo-phtisiologie du Centre Hospitalier Universitaire du Point-G, Bamako, Mali
| | - Bakary Konate
- Programme National de Lutte Contre la Tuberculose (PNLT), Ministère de la Santé et de l'hygiène Publique, Bamako, Mali
| | - Moumine Sanogo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme Combo Georges Togo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fatimata Camara
- Laboratoire National de Référence des Mycobactéries (LNR), Institut National de Recherche en Santé Publique (INRSP), Bamako, Mali
| | - Gaoussou Berthe
- Service de Pneumo-phtisiologie du Centre Hospitalier Universitaire du Point-G, Bamako, Mali
| | - Dianguina Soumaré
- Service de Pneumo-phtisiologie du Centre Hospitalier Universitaire du Point-G, Bamako, Mali
| | - Bocar Baya
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa Goita
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- Global Health, Northwestern University, Chicago, IL, USA
| | - Michael Belson
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Susan Orsega
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sounkalo Dao
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Sophia Siddiqui
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Bouke C de Jong
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Seydou Doumbia
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- University Clinical Research Center (UCRC)-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| |
Collapse
|
47
|
Okoi C, Anderson STB, Antonio M, Mulwa SN, Gehre F, Adetifa IMO. Non-tuberculous Mycobacteria isolated from Pulmonary samples in sub-Saharan Africa - A Systematic Review and Meta Analyses. Sci Rep 2017; 7:12002. [PMID: 28931915 PMCID: PMC5607231 DOI: 10.1038/s41598-017-12175-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/05/2017] [Indexed: 01/29/2023] Open
Abstract
Pulmonary non-tuberculous mycobacterial (NTM) disease epidemiology in sub-Saharan Africa is not as well described as for pulmonary tuberculosis. Earlier reviews of global NTM epidemiology only included subject-level data from one sub-Saharan Africa country. We systematically reviewed the literature and searched PubMed, Embase, Popline, OVID and Africa Wide Information for articles on prevalence and clinical relevance of NTM detection in pulmonary samples in sub-Saharan Africa. We applied the American Thoracic Society/Infectious Disease Society of America criteria to differentiate between colonisation and disease. Only 37 articles from 373 citations met our inclusion criteria. The prevalence of pulmonary NTM colonization was 7.5% (95% CI: 7.2%–7.8%), and 75.0% (2325 of 3096) occurred in males, 16.5% (512 of 3096) in those previously treated for tuberculosis and Mycobacterium avium complex predominated (27.7% [95% CI: 27.2–28.9%]). In seven eligible studies, 27.9% (266 of 952) of participants had pulmonary NTM disease and M. kansasii with a prevalence of 69.2% [95% CI: 63.2–74.7%] was the most common cause of pulmonary NTM disease. NTM species were unidentifiable in 29.2% [2,623 of 8,980] of isolates. In conclusion, pulmonary NTM disease is a neglected and emerging public health disease and enhanced surveillance is required.
Collapse
Affiliation(s)
- Catherine Okoi
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia
| | | | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah N Mulwa
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Ifedayo M O Adetifa
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom. .,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. .,College of Medicine University of Lagos, Lagos, Nigeria.
| |
Collapse
|
48
|
Nasiri M, Dabiri H, Fooladi A, Amini S, Hamzehloo G, Feizabadi M. High rates of nontuberculous mycobacteria isolation from patients with presumptive tuberculosis in Iran. New Microbes New Infect 2017; 21:12-17. [PMID: 29188063 PMCID: PMC5695646 DOI: 10.1016/j.nmni.2017.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) can cause disease which can be indistinguishable from tuberculosis (TB), posing a diagnostic and therapeutic challenge, particularly in low- and middle-income settings. We aimed to investigate the mycobacterial agents associated with presumptive clinical pulmonary TB in Iran. A total of 410 mycobacterial isolates, obtained between March 2014 and January 2016, from 7600 clinical samples taken from consecutive cases of presumptive diagnosis of TB were identified. Phenotypic and molecular tests were used to identify the isolated organisms to the species level. Single-locus and multilocus sequence analysis based on 16S rRNA, rpoB, hsp65 and ITS locus were used to confirm the results. Of 410 consecutive strains isolated from suspected TB subjects, 62 isolates (15.1%) were identified as NTM. Patients with positive NTM cultures met American Thoracic Society diagnostic criteria for NTM disease. Mycobacterium simiae was the most frequently encountered (38.7%), followed by Mycobacterium fortuitum (19.3%), M. kansasii (17.7%) and M. avium complex (8.0%). Isolation of NTM, including M. simiae, from suspected TB cases is a serious public health problem and merits further attention by health authorities, physicians and microbiologists.
Collapse
Affiliation(s)
- M.J. Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Iran
| | - H. Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Iran
| | - A.A.I. Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Iran
| | - S. Amini
- Regional Tuberculosis Reference Laboratory, Iran
| | - G. Hamzehloo
- Regional Tuberculosis Reference Laboratory, Iran
| | - M.M. Feizabadi
- Department of Microbiology, School of Medicine, Iran
- Thoracic Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding author: M. M. Feizabadi, Department of Microbiology, Tehran University of Medical Sciences, School of Medicine, Tehran, IranDepartment of MicrobiologyTehran University of Medical SciencesSchool of MedicineTehranIran
| |
Collapse
|
49
|
Mnyambwa NP, Ngadaya ES, Kimaro G, Kim DJ, Kazwala R, Petrucka P, Mfinanga SG. Assessment of sputum smear-positive but culture-negative results among newly diagnosed pulmonary tuberculosis patients in Tanzania. Int J Gen Med 2017; 10:199-205. [PMID: 28744153 PMCID: PMC5513826 DOI: 10.2147/ijgm.s137469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Diagnosis of pulmonary tuberculosis (TB) in technology-limited countries is widely achieved by smear microscopy, which has limited sensitivity and specificity. The frequency and clinical implication of smear-positive but culture-negative among presumptive TB patients remains unclear. A cross-sectional substudy was conducted which aimed to identify the proportion of nontuberculous mycobacteria (NTM) infections among 94 "smear-positive culture-negative" patients diagnosed between January 2013 and June 2016 in selected health facilities in Tanzania. Out of 94 sputa, 25 (26.60%) were GeneXpert® mycobacteria TB positive and 11/94 (11.70%) repeat-culture positive; 5 were Capilia TB-Neo positive and confirmed by GenoType MTBC to be Mycobacterium tuberculosis/Mycobacterium canettii. The remaining 6 Capilia TB-Neo negative samples were genotyped by GenoType® CM/AS, identifying 3 (3.19%) NTM, 2 Gram positive bacteria, and 1 isolate testing negative, together, making a total of 6/94 (6.38%) confirmed false smear-positives. Twenty-eight (29.79%) were confirmed TB cases, while 60 (63.83%) remained unconfirmed cases. Out of 6 (6.38%) patients who were HIV positive, 2 patients were possibly coinfected with mycobacteria. The isolation of NTM and other bacteria among smear-positive culture-negative samples and the presence of over two third of unconfirmed TB cases emphasize the need of both advanced differential TB diagnostic techniques and good clinical laboratory practices to avoid unnecessary administration of anti-TB drugs.
Collapse
Affiliation(s)
- Nicholaus Peter Mnyambwa
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Esther S Ngadaya
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Godfather Kimaro
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Dong-Jin Kim
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Rudovick Kazwala
- Department of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Pammla Petrucka
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- College of Nursing, University of Saskatchewan, Saskatoon, Canada
| | - Sayoki G Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| |
Collapse
|
50
|
Nishiuchi Y, Iwamoto T, Maruyama F. Infection Sources of a Common Non-tuberculous Mycobacterial Pathogen, Mycobacterium avium Complex. Front Med (Lausanne) 2017; 4:27. [PMID: 28326308 PMCID: PMC5339636 DOI: 10.3389/fmed.2017.00027] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Numerous studies have revealed a continuous increase in the worldwide incidence and prevalence of non-tuberculous mycobacteria (NTM) diseases, especially pulmonary Mycobacterium avium complex (MAC) diseases. Although it is not clear why NTM diseases have been increasing, one possibility is an increase of mycobacterial infection sources in the environment. Thus, in this review, we focused on the infection sources of pathogenic NTM, especially MAC. The environmental niches for MAC include water, soil, and dust. The formation of aerosols containing NTM arising from shower water, soil, and pool water implies that these niches can be infection sources. Furthermore, genotyping has shown that clinical isolates are identical to environmental ones from household tap water, bathrooms, potting soil, and garden soil. Therefore, to prevent and treat MAC diseases, it is essential to identify the infection sources for these organisms, because patients with these diseases often suffer from reinfections and recurrent infections with them. In the environmental sources, MAC and other NTM organisms can form biofilms, survive within amoebae, and exist in a free-living state. Mycobacterial communities are also likely to occur in these infection sources in households. Water distribution systems are a transmission route from natural water reservoirs to household tap water. Other infection sources include areas with frequent human contact, such as soil and bathrooms, indicating that individuals may carry NTM organisms that concomitantly attach to their household belongings. To explore the mechanisms associated with the global spread of infection and MAC transmission routes, an epidemiological population-wide genotyping survey would be very useful. A good example of the power of genotyping comes from M. avium subsp. hominissuis, where close genetic relatedness was found between isolates of it from European patients and pigs in Japan and Europe, implying global transmission of this bacterium. It is anticipated that whole genome sequencing technologies will improve NTM surveys so that the mechanisms for the global spread of MAC disease will become clearer in the near future. Better understanding of the niches exploited by MAC and its ecology is essential for preventing MAC infections and developing new methods for its effective treatment and elimination.
Collapse
Affiliation(s)
- Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School , Toyonaka , Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health , Kobe , Japan
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine and Faculty of Medicine, Kyoto University , Kyoto , Japan
| |
Collapse
|