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Yin Y, Zhu P, Guo Y, Li Y, Chen H, Liu J, Sun L, Ma S, Hu C, Wang H. Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing. EBioMedicine 2024; 107:105307. [PMID: 39226681 DOI: 10.1016/j.ebiom.2024.105307] [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: 04/13/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Shotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice. METHODS We used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed. FINDINGS mp-tNGS and hc-tNGS took 10.3 and 16 h, respectively, with low sequencing data sizes of 0.1 M and 1 M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450 CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P < 0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS. INTERPRETATION tNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections. FUNDING National Natural Science Foundation of China (81625014 and 82202535).
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Affiliation(s)
- Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Pengyuan Zhu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China
| | - Lingxiao Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Dahl VN, Pedersen AA, Norman A, Rasmussen EM, van Ingen J, Andersen AB, Wejse CM, Lillebaek T. Clinical Significance, Species Distribution, and Temporal Trends of Nontuberculous Mycobacteria, Denmark, 1991-2022. Emerg Infect Dis 2024; 30:1755-1762. [PMID: 39173666 PMCID: PMC11346989 DOI: 10.3201/eid3009.240095] [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: 08/24/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) are emerging as notable causative agents of opportunistic infections. To examine clinical significance, species distribution, and temporal trends of NTM in Denmark, we performed a nationwide register-based study of all unique persons with NTM isolated in the country during 1991-2022. We categorized patients as having definite disease, possible disease, or isolation by using a previously validated method. The incidence of pulmonary NTM increased throughout the study period, in contrast to earlier findings. Mycobacterium malmoense, M. kansasii, M. szulgai, and M. avium complex were the most clinically significant species based on microbiologic findings; M. avium dominated in incidence. This study shows the need for surveillance for an emerging infection that is not notifiable in most countries, provides evidence to support clinical decision-making, and highlights the importance of not considering NTM as a single entity.
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3
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Capstick T, Hurst R, Keane J, Musaddaq B. Supporting Patients with Nontuberculous Mycobacterial Pulmonary Disease: Ensuring Best Practice in UK Healthcare Settings. PHARMACY 2024; 12:126. [PMID: 39195855 PMCID: PMC11359432 DOI: 10.3390/pharmacy12040126] [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: 04/17/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
Nontuberculous mycobacterial pulmonary disease (NTM-PD) results from opportunistic lung infections by mycobacteria other than Mycobacterium tuberculosis or Mycobacterium leprae species. Similar to many other countries, the incidence of NTM-PD in the United Kingdom (UK) is on the rise for reasons that are yet to be determined. Despite guidelines established by the American Thoracic Society (ATS), the Infectious Diseases Society of America, and the British Thoracic Society, NTM-PD diagnosis and management remain a significant clinical challenge. In this review article, we comprehensively discuss key challenges in NTM-PD diagnosis and management, focusing on the UK healthcare setting. We also propose countermeasures to overcome these challenges and improve the detection and treatment of patients with NTM-PD.
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Affiliation(s)
| | - Rhys Hurst
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK;
| | - Jennie Keane
- Essex Partnership University NHS Foundation Trust (EPUT), Rochford SS4 1DD, UK;
| | - Besma Musaddaq
- Department of Radiology, Royal Free Hospital NHS Foundation Trust, London NW3 2QG, UK;
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4
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Aksamit TR, Locantore N, Addrizzo-Harris D, Ali J, Barker A, Basavaraj A, Behrman M, Brunton AE, Chalmers S, Choate R, Dean NC, DiMango A, Fraulino D, Johnson MM, Lapinel NC, Maselli DJ, McShane PJ, Metersky ML, Miller BE, Naureckas ET, O'Donnell AE, Olivier KN, Prusinowski E, Restrepo MI, Richards CJ, Rhyne G, Schmid A, Solomon GM, Tal-Singer R, Thomashow B, Tino G, Tsui K, Varghese SA, Warren HE, Winthrop K, Zha BS. Five-Year Outcomes among U.S. Bronchiectasis and NTM Research Registry Patients. Am J Respir Crit Care Med 2024; 210:108-118. [PMID: 38668710 DOI: 10.1164/rccm.202307-1165oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/24/2024] [Indexed: 07/02/2024] Open
Abstract
Rationale: Nontuberculous mycobacteria (NTM) are prevalent among patients with bronchiectasis. However, the long-term natural history of patients with NTM and bronchiectasis is not well described. Objectives: To assess the impact of NTM on 5-year clinical outcomes and mortality in patients with bronchiectasis. Methods: Patients in the Bronchiectasis and NTM Research Registry with ⩾5 years of follow-up were eligible. Data were collected for all-cause mortality, lung function, exacerbations, hospitalizations, and disease severity. Outcomes were compared between patients with and without NTM at baseline. Mortality was assessed using Cox proportional hazards models and the log-rank test. Measurements and Main Results: In total, 2,634 patients were included: 1,549 (58.8%) with and 1,085 (41.2%) without NTM at baseline. All-cause mortality (95% confidence interval) at Year 5 was 12.1% (10.5%, 13.7%) overall, 12.6% (10.5%, 14.8%) in patients with NTM, and 11.5% (9.0%, 13.9%) in patients without NTM. Independent predictors of 5-year mortality were baseline FEV1 percent predicted, age, hospitalization within 2 years before baseline, body mass index, and sex (all P < 0.01). The probabilities of acquiring NTM or Pseudomonas aeruginosa were approximately 4% and 3% per year, respectively. Spirometry, exacerbations, and hospitalizations were similar, regardless of NTM status, except that annual exacerbations were lower in patients with NTM (P < 0.05). Conclusions: Outcomes, including exacerbations, hospitalizations, rate of loss of lung function, and mortality rate, were similar across 5 years in patients with bronchiectasis with or without NTM.
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Affiliation(s)
- Timothy R Aksamit
- COPD Foundation, Washington, District of Columbia
- Pulmonary Disease and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | | | | | - Juzar Ali
- Health Sciences Center, Louisiana State University, New Orleans, Louisiana
| | - Alan Barker
- Division of Pulmonary and Critical Care, School of Medicine, Oregon Health and Science University, Portland, Oregon
| | | | - Megan Behrman
- University of Kansas Medical Center, University of Kansas, Kansas City, Kansas
| | | | - Sarah Chalmers
- Pulmonary Disease and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | - Radmila Choate
- COPD Foundation, Washington, District of Columbia
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, Kentucky
| | - Nathan C Dean
- Schmidt Chest Clinic, Intermountain Medical Center, Murray, Utah
| | - Angela DiMango
- Center for Chest Disease, College of Physicians and Surgeons, Columbia University, New York, New York
| | - David Fraulino
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Connecticut, Farmington, Connecticut
| | | | - Nicole C Lapinel
- Section of Pulmonary, Critical Care Medicine, Department of Medicine, Northwell Health, New Hyde Park, New York
| | | | - Pamela J McShane
- Health Science Center, University of Texas at Tyler, Tyler, Texas
| | - Mark L Metersky
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Connecticut, Farmington, Connecticut
| | | | - Edward T Naureckas
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Anne E O'Donnell
- Georgetown University Medical Center, Georgetown University, Washington, District of Columbia
| | - Kenneth N Olivier
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Elly Prusinowski
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | | | - Christopher J Richards
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gloria Rhyne
- Department of Infectious Disease, Oregon Health and Science University - Portland State University School of Public Health, Oregon Health and Science University School of Medicine, Portland, Oregon; and
| | - Andreas Schmid
- University of Kansas Medical Center, University of Kansas, Kansas City, Kansas
| | - George M Solomon
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Byron Thomashow
- Center for Chest Disease, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Gregory Tino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin Tsui
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Sumith Abraham Varghese
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Connecticut, Farmington, Connecticut
| | - Heather E Warren
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, University of Connecticut, Farmington, Connecticut
| | - Kevin Winthrop
- Department of Infectious Disease, Oregon Health and Science University - Portland State University School of Public Health, Oregon Health and Science University School of Medicine, Portland, Oregon; and
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Tsiolakkis G, Liontos A, Filippas-Ntekouan S, Matzaras R, Theodorou E, Vardas M, Vairaktari G, Nikopoulou A, Christaki E. Mycobacterium marinum: A Case-Based Narrative Review of Diagnosis and Management. Microorganisms 2023; 11:1799. [PMID: 37512971 PMCID: PMC10384600 DOI: 10.3390/microorganisms11071799] [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: 05/03/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Skin and soft tissue infections caused by non-tuberculous mycobacteria are occurring more frequently in recent years. However, chronic skin and soft tissue lesions present a challenge for clinicians, as the diagnostic work-up and definitive diagnosis require knowledge and available laboratory resources. We present here the case of a 66-year-old male patient who presented with painful abscess-like nodules on his right hand and forearm, which worsened after treatment with an anti-TNF-a agent. The fluid specimen taken from the lesion was positive for mycobacteria according to the acid-fast stain. Mycobacterium marinum was identified, first by next-generation sequencing and finally grown on culture, after eight weeks. Acknowledging the complexity of diagnosing and managing infections by non-tuberculous mycobacteria, and especially Mycobacterium marinum, we provide a review of the current epidemiology, clinical characteristics, diagnosis and management of Mycobacterium marinum infection.
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Affiliation(s)
- Giorgos Tsiolakkis
- Department of Internal Medicine, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Angelos Liontos
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | - Sempastian Filippas-Ntekouan
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | - Rafail Matzaras
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | | | - Michail Vardas
- School of Medicine, University of Cyprus, Nicosia 2029, Cyprus
| | | | - Anna Nikopoulou
- Department of Internal Medicine, G. Papanikolaou General Hospital of Thessaloniki, 57010 Thessaloniki, Greece
| | - Eirini Christaki
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
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Markanović M, Makek MJ, Glodić G, Kuliš T, Mareković I. Evaluation and clinical impact of MALDI Biotyper Mycobacteria Library v6.0 for identification of nontuberculous mycobacteria by MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4915. [PMID: 37010443 DOI: 10.1002/jms.4915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Major challenges in the identification of non-tuberculous mycobacteria (NTM) by MALDI-TOF MS include protein extraction protocol and updating of the NTM database. The aim of this study was to evaluate MALDI Biotyper Mycobacteria Library v6.0 (Bruker Daltonics GmbH, Bremen, Germany) for identification of clinical NTM isolates and its impact on clinical management. NTM isolates cultivated from clinical samples in 101 patients were identified simultaneously by PCR-reverse hybridization (Hain Lifescience GmbH, Nehren, Germany) as a routinely used reference molecular method and using MALDI Biotyper Microflex LT/SH after protein extraction. Each isolate was applied to eight spots, and mean scores were used in analysis. MALDI-TOF MS obtained correct identification to the species level for 95 (94.06%) NTM isolates. The majority of correctly identified isolates (92/95; 96.84%) were identified with high-confidence score of ≥1.80 and only 3.16% (3/95) with a score of <1.80. Mean value ± SD of RGM NTM isolates (2.127 ± 0.172) was statistically significant higher in comparison to SGM NTM isolates (2.027 ± 0.142) with a p value of 0.007. In comparison to PCR-reverse hybridization, discordant identification results by MALDI-TOF MS were found in six (6/101; 5.94%) NTM isolates for which clinical data were analyzed. We demonstrated a high confidence NTM identifications using Mycobacterium Library v 6.0 on routine clinical isolates. This is the first study that analyzed MALDI-TOF MS identification results of NTM isolates in the context of clinical data, and it showed that MALDI-TOF MS with its updated databases could help clarify the epidemiology, clinical characteristics, and course of infections caused by less frequent NTM species.
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Affiliation(s)
- Manda Markanović
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Mateja Janković Makek
- School of Medicine, University of Zagreb, Zagreb, 10 000, Croatia
- Department of Respiratory Diseases, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Goran Glodić
- Department of Respiratory Diseases, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Tomislav Kuliš
- Department of Urology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
- School of Medicine, University of Zagreb, Zagreb, 10 000, Croatia
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7
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Schildkraut JA, Coolen JPM, Severin H, Koenraad E, Aalders N, Melchers WJG, Hoefsloot W, Wertheim HFL, van Ingen J. MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care. J Clin Microbiol 2023; 61:e0131822. [PMID: 36840602 PMCID: PMC10035320 DOI: 10.1128/jcm.01318-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.
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Affiliation(s)
- Jodie A Schildkraut
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jordy P M Coolen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heleen Severin
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ellen Koenraad
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole Aalders
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter Hoefsloot
- Radboudumc Center for Infectious Diseases, Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heiman F L Wertheim
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
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8
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Wang J, Xu H, Wang X, Lan J. Rapid diagnosis of non-tuberculous mycobacterial pulmonary diseases by metagenomic next-generation sequencing in non-referral hospitals. Front Cell Infect Microbiol 2023; 12:1083497. [PMID: 36760234 PMCID: PMC9902348 DOI: 10.3389/fcimb.2022.1083497] [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: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Objectives The incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has increased steadily globally, but the current culture-based diagnosis of NTM-PD is difficult and time-consuming, leading to a high possibility of misdiagnosis. Therefore, new methods should be introduced to improve the processes for clinical diagnosis of this disease. Methods Our retrospective observational study enrolled 12 NTM-PD patients who were identified by way of metagenomic next-generation sequencing (mNGS), as well as the characteristic radiological presentation of slowly progressed, usually concomitant bronchiectasis, small cavitary opacity, and multiple nodules that respond poorly to empirical antibiotic therapy. These patients received the recommended drug regimen based on the identified non-tuberculous mycobacteria (NTM) species. Clinical data, including symptoms, laboratory tests, dynamic computed tomography imaging, treatment, and outcome, were recorded and analyzed. Results The results of mNGS were all positive, with the standard specifically mapped read numbers (SDSMRN) of NTM ranging from 1 to 766; this was confirmed in six patients via quantitative polymerase chain reaction (qPCR) analysis. The duration fromsample collection tomNGS results was 1-4 days. Among our 12 patients (except for one lost to follow-up) the CT imaging for 11 patients showed significant absorption of lesions. Conclusions Our results draw attention to NTM infection as a possible cause of community-acquired pneumonia, especially in patients with suggestive radiological presentation and poor responses to empirical antibiotic therapy. Our study also indicated that mNGS represented a potentially effective tool for the rapid identification of NTM in the respiratory sample. Improved clinician awareness combined with the utilization of mNGS could guide earlier diagnosis and targeted treatment, and finally improved the prognoses of patients with NTM-PD.
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Affiliation(s)
- Jing Wang
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Xi Wang
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Lan
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Jian Lan,
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9
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Pastrone L, Curtoni A, Criscione G, Scaiola F, Bottino P, Guarrasi L, Iannaccone M, Timke M, Costa C, Cavallo R. Evaluation of Two Different Preparation Protocols for MALDI-TOF MS Nontuberculous Mycobacteria Identification from Liquid and Solid Media. Microorganisms 2023; 11:microorganisms11010120. [PMID: 36677412 PMCID: PMC9866535 DOI: 10.3390/microorganisms11010120] [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: 12/04/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool for NTM identification, and its use is rapidly growing. We evaluated the newly introduced MBT Mycobacteria kit (MBT) and the MycoEx preparation protocol (Bruker Daltonics, Germany) for NTM MALDI-TOF MS identification using LPA results as a reference. Fifty NTM grown on 7H11 agar and MGIT broth were analyzed with both protocols using the Bruker Microflex® LT MALDI-TOF MS (Bruker Daltonics) instrument. MBT and MycoEx provided identification results in 97.0% and 95.0% of the cases, respectively. With both protocols, 100% of the provided results agreed with LPA with no registered mismatch. MBT achieved an elevated number of highly probable identifications (88.0% vs. 83.0%) and a higher reproducibility rate of correct results (86.6% vs. 75.8%) in comparison to MycoEx. This study provides results about MBT performance for liquid and solid media, underlining the strengths and weakness under different conditions. Our results suggest that MALDI-TOF MS could provide a great advantage for timely and cost-saving NTM identification with potential implications for patient outcome.
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Affiliation(s)
- Lisa Pastrone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Correspondence: ; Tel.: +39-011-633-7005
| | - Giulia Criscione
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Francesca Scaiola
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Paolo Bottino
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Luisa Guarrasi
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Iannaccone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Markus Timke
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
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10
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Using Vitek MS v3.0 To Identify Nontuberculous Mycobacteria in Liquid Media in a Clinical Microbiology Laboratory. Microbiol Spectr 2022; 10:e0201822. [PMID: 36287015 PMCID: PMC9769768 DOI: 10.1128/spectrum.02018-22] [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] [Indexed: 01/06/2023] Open
Abstract
Recently, the incidence of diseases caused by nontuberculous mycobacteria (NTM) has been increasing worldwide, especially in immunocompromised patients and those with potential chronic lung disease. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study aimed to evaluate the performance of Vitek MS v3.0 by isolating NTM directly from automated liquid medium systems using patient samples. A total of 855 Mycobacterium growth indicator tube (MGIT)-positive liquid cultures were investigated. Among them, 658 (77.0%) liquid cultures were correctly identified to the species, group, or complex level, 192 (23.0%) resulted in no identification, and 5 (0.6%) were misidentified at the species level. DNA sequencing identified 855 NTM isolates from liquid cultures, comprising 316 isolates of rapidly growing mycobacteria (RGM) and 539 isolates of slow-growing mycobacteria (SGM). Using the Vitek MS system, the RGM integral identification rate (276/316 [87.34%]) was higher than the SGM rate (381/539 [70.69%]) (P < 0.01). It was also higher than the SGM rate for all MGIT report-positive periods. These results indicate that the Vitek MS v3.0 system can rapidly identify NTM species from liquid cultures. Further validation using molecular techniques is required. IMPORTANCE Rapid and accurate identification of nontuberculous mycobacteria (NTM) is essential for diagnosis, appropriate therapy, and infection control. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study reported a clinical validation of the Vitek MS V3.0 system for identification of NTM isolates from 855 MGIT-positive liquid cultures which contained relatively large NTM types. Vitek MS v3.0 showed a promising rate for identification NTM isolates in positive liquid cultures. Vitek MS v3.0 had a better performance with RGM than with SGM. Vitek MS v3.0 results included "unidentified" or "misidentified" NTM isolates, which would also serve as an important reference for future optimization of this system. Vitek MS v3.0 represented a valuable technique for NTM identification from positive liquid cultures.
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Ganga RT, Sharma P, Pati SK, Behera AK, Reddy SK. Mycobacterium kansasaii and Mycobacterium scrofulaceum dual pulmonary infection in an immunocompetent male: first report from India. Monaldi Arch Chest Dis 2022. [DOI: 10.4081/monaldi.2022.2371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
A 57-year-old farmer presented with chronic cough and recurrent hemoptysis, previously treated for sputum positive pulmonary tuberculosis. Referred to us for evaluation of drug resistant tuberculosis as his sputum was persistently positive for acid fast bacilli along with radiological worsening even after 6 months of antitubercular treatment. Bronchoalveolar lavage was done and he was diagnosed with a rare mixed non-tuberculous mycobacyteria (NTM) pulmonary infection despite no immune dysfunction. He was successfully treated with multidrug regimen of rifampicin, isoniazid, ethambutol and clarithromycin.
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12
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Verma AK, Arora VK. Non-tuberculous mycobacterial infections in geriatric patients-A neglected and emerging problem. Indian J Tuberc 2022; 69 Suppl 2:S235-S240. [PMID: 36400516 DOI: 10.1016/j.ijtb.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The diseases caused by Non-tuberculous mycobacteria (NTM) has increased steadily in the last two decades. Increase in incidence of NTM infections are being reported in elderly people as they are more susceptible and often experiencing high morbidity. There is prediction that NTM infections will further rise because of expected increase in elderly population by 2050. Given the importance of NTM infection in the elderly, the interest in studying NTM characteristics in the aged population is increasing. In this review, we summarize the characteristics of NTM infection among elderly patients. We focus on epidemiology, clinical presentation, and treatment options of NTM in this age group. We highlight the differences in the diagnosis and treatment between rapid and slow growing mycobacterial infections. The current recommendations for treatment of NTM have been discussed. Finally, we have reviewed the prognosis of NTM disease in elderly patients.
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Affiliation(s)
- Ajoy Kumar Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India.
| | - Vijay Kumar Arora
- Santosh University, NCR Delhi, Formerly Director - National Institute of TB & Respiratory Diseases (LRS), Formerly - Additional DGHS, Goverment of India, India
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Gorospe-Sarasúa L, Alarcón-Rodríguez J, Tato-Díez M, Dronda F. Disseminated Mycobacterium avium complex infection: microbiological confirmation by «percutaneous» sputum induction following the intracavitary instillation of normal saline. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:456-458. [PMID: 35659773 DOI: 10.1016/j.eimce.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 06/15/2023]
Affiliation(s)
- Luis Gorospe-Sarasúa
- Servicio de Radiodiagnóstico, Hospital Universitario Ramón y Cajal, Madrid, Spain.
| | | | - Marta Tato-Díez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Fernando Dronda
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal, Madrid, Spain
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Zhou Y, Mu W, Zhang J, Wen SW, Pakhale S. Global prevalence of non-tuberculous mycobacteria in adults with non-cystic fibrosis bronchiectasis 2006-2021: a systematic review and meta-analysis. BMJ Open 2022; 12:e055672. [PMID: 35914904 PMCID: PMC9345037 DOI: 10.1136/bmjopen-2021-055672] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To accurately estimate the global prevalence of non-tuberculous mycobacteria (NTM) in adults with non-cystic fibrosis (non-CF) bronchiectasis and to determine the proportion of NTM species and subspecies in clinical patients from 2006 to 2021. DESIGN Systematic review and meta-analysis using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. DATA SOURCES Medline, Embase, Cochrane Library and Web of Science were searched for articles published between 2006 and 2021. ELIGIBILITY CRITERIA FOR SELECTING STUDIES We included all the prospective or retrospective studies without language restrictions and all patients were adults (≥18 years of age) with non-CF bronchiectasis. The studies estimated the effect size of the prevalence of NTM with a sample size ≥40, and patients were registered in and after 2006. DATA EXTRACTION AND SYNTHESIS Two reviewers screened the titles, abstracts and full texts independently. Relevant information was extracted and curated into tables. Risk of bias was evaluated following the Cochrane Collaboration's tool. Meta-analysis was performed with software R Statistics V.3.6.3 using random effect model with 95% CI. I2 index and Q statistics were calculated to assess the heterogeneity, and mixed-effects meta-regression analyses were performed to identify the sources of heterogeneity. The proportions of NTM subspecies were examined using Shapiro-Wilk normality test in R. RESULTS Of all the 2014 studies yielded, 24 met the inclusion criteria. Of these, 14 were identified to be randomised controlled studies and included for an accurate estimation. The global prevalence of NTM in adults with non-CF bronchiectasis from 2006 to 2021 was estimated to be approximately 10%, with great variations primarily due to geographical location. Mycobacterium avium complex was the most common subspecies, followed by Mycobacterium simiae and Mycobacterium gordonae. CONCLUSIONS The prevalence of NTM in adults with non-CF bronchiectasis has been on the rise and the most common subspecies changed greatly in recent years. More cohort studies should be done in many countries and regions for future estimates. PROSPERO REGISTRATION NUMBER CRD42020168473.
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Affiliation(s)
- Yunchun Zhou
- Department of Pulmonary and Critical Care Medicine, People's Hospital of Yuxi City, Yuxi, Yunnan, China
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Wei Mu
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jihua Zhang
- Department of Pulmonary and Critical Care Medicine, People's Hospital of Yuxi City, Yuxi, Yunnan, China
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Shi Wu Wen
- The Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Smita Pakhale
- The Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Division of Respiratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
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15
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Mellett M, Thornton CS, Barss L, Lim RK, Fisher DA, Jarand J, Field SK. Prevalence of adverse electrophysiologic and audiometric changes in nontuberculous mycobacterium treatment regimens. Eur Respir J 2022; 60:2200167. [PMID: 35863768 DOI: 10.1183/13993003.00167-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/04/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Madeline Mellett
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- co-first authors
| | - Christina S Thornton
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- co-first authors
| | - Leila Barss
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel K Lim
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Dina A Fisher
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Julie Jarand
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stephen K Field
- Division of Respirology, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Park YE, Park SY, Jhun BW, Park Y, Kang YA, Park J, Kwak N, Yim JJ, Shim TS, Jo KW. Treatment outcome of continuation of intravenous amikacin for Mycobacterium abscessus pulmonary disease with a persistent culture positivity after the treatment initiation. J Infect Chemother 2022; 28:1098-1104. [DOI: 10.1016/j.jiac.2022.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/24/2022] [Accepted: 03/25/2022] [Indexed: 10/18/2022]
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Nontuberculous Mycobacterial Resistance to Antibiotics and Disinfectants: Challenges Still Ahead. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8168750. [PMID: 35257011 PMCID: PMC8898113 DOI: 10.1155/2022/8168750] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022]
Abstract
The mortality incidence from nontuberculous mycobacteria (NTM) infections has been steadily developing globally. These bacterial agents were once thought to be innocent environmental saprophytic that are only dangerous to patients with defective lungs or the immunosuppressed. Nevertheless, the emergence of highly resistant NTM to different antibiotics and disinfectants increased the importance of these agents in the health system. Currently, NTM frequently infect seemingly immunocompetent individuals at rising rates. This is of concern as the resistant NTM are difficult to control and treat. The details behind this NTM development are only beginning to be clarified. The current study will provide an overview of the most important NTM resistance mechanisms to not only antibiotics but also the most commonly used disinfectants. Such evaluations can open new doors to improving control strategies and reducing the risk of NTM infection. Moreover, further studies are crucial to uncover this association.
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Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification. Sci Rep 2022; 12:1237. [PMID: 35075208 PMCID: PMC8786948 DOI: 10.1038/s41598-022-05315-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/11/2022] [Indexed: 11/08/2022] Open
Abstract
The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Löwenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score ≥ 1.6 was obtained for 100% of isolates in 5 laboratories (68.2–98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification.
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19
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Management of patients with pulmonary mycobacteriosis in France: a multicenter retrospective cohort study. BMC Pulm Med 2021; 21:333. [PMID: 34702233 PMCID: PMC8549171 DOI: 10.1186/s12890-021-01701-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 01/15/2023] Open
Abstract
Background Recent studies report very low adherence of practitioners to ATS/IDSA recommendations for the treatment of nontuberculous mycobacteria pulmonary disease (NTM-PD), as well as a great variability of practices. Type of management could impact prognosis. Methods To evaluate management and prognosis of patients with NTM-PD cases with respect to ATS recommendations, we conducted a multicenter retrospective cohort study (18 sentinel sites distributed throughout France), over a period of six years. We collected clinical, radiological, microbiological characteristics, management and outcome of the patients (especially death or not). Results 477 patients with NTM-PD were included. Respiratory comorbidities were found in 68% of cases, tuberculosis sequelae in 31.4% of patients, and immunosuppression in 16.8% of cases. The three most common NTM species were Mycobacterium avium complex (60%), M. xenopi (20%) and M. kansasii (5.7%). Smear-positive was found in one third of NTM-PD. Nodulobronchiectatic forms were observed in 54.3% of cases, and cavitary forms in 19.1% of patients. Sixty-three percent of patients were treated, 72.4% of patients with smear-positive samples, and 57.5% of patients with smear-negative samples. Treatment was in adequacy with ATS guidelines in 73.5%. The 2-year mortality was 14.4%. In the Cox regression, treatment (HR = 0.51), age (HR = 1.02), and M. abscessus (3.19) appeared as the 3 significant independent prognostic factors. Conclusion These findings highlight the adequacy between French practices and the ATS/IDSA guidelines. Treatment was associated with a better survival. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01701-5.
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20
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Mycobacterium Growth Indicator Tube Time-To-Positivity Can Serve As an Early Biomarker of Treatment Response in Mycobacterium avium Complex Pulmonary Disease. Chest 2021; 161:370-372. [PMID: 34391756 PMCID: PMC8941609 DOI: 10.1016/j.chest.2021.08.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/15/2021] [Accepted: 08/08/2021] [Indexed: 11/24/2022] Open
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21
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Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and 193 species of NTM have been discovered thus far. NTM species vary in virulence from benign environmental organisms to difficult-to-treat human pathogens. Pulmonary infections remain the most common manifestation of NTM disease in humans and bronchiectasis continues to be a major risk factor for NTM pulmonary disease (NTM PD). This article will provide a useful introduction and framework for clinicians involved in the management of bronchiectasis and NTM. It includes an overview of the epidemiology, pathogenesis, diagnosis, and management of NTM PD. We will address the challenges faced in the diagnosis of NTM PD and the importance of subspeciation in guiding treatment and follow-up, especially in Mycobacterium abscessus infections. The treatment of both Mycobacterium avium complex and M. abscessus, the two most common NTM species known to cause disease, will be discussed in detail. Elements of the recent ATS/ERS/ESCMID/IDSA NTM guidelines published in 2020 will also be reviewed.
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Affiliation(s)
- Shera Tan
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore, Singapore
| | - Shannon Kasperbauer
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado
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22
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Gorospe-Sarasúa L, Alarcón-Rodríguez J, Tato-Díez M, Dronda F. Disseminated Mycobacterium avium complex infection: microbiological confirmation by «percutaneous» sputum induction following the intracavitary instillation of normal saline. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00206-8. [PMID: 34256971 DOI: 10.1016/j.eimc.2021.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Luis Gorospe-Sarasúa
- Servicio de Radiodiagnóstico, Hospital Universitario Ramón y Cajal, Madrid, España.
| | | | - Marta Tato-Díez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Madrid, España
| | - Fernando Dronda
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal, Madrid, España
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23
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Pennington KM, Vu A, Challener D, Rivera CG, Shweta FNU, Zeuli JD, Temesgen Z. Approach to the diagnosis and treatment of non-tuberculous mycobacterial disease. J Clin Tuberc Other Mycobact Dis 2021; 24:100244. [PMID: 34036184 PMCID: PMC8135042 DOI: 10.1016/j.jctube.2021.100244] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Non-tuberculous mycobacteria (NTM) is a collective name given to a group of more than 190 species of Mycobacterium. The clinical presentation for most NTM infections is non-specific, often resulting in delayed diagnosis. Further complicating matters is that NTM organisms can be difficult to isolate. Medications used to treat NTM infection can be difficult for patients to tolerate, and prolonged courses of anti-mycobacterial therapy are often required for adequate suppression or eradication. Herein, we review different NTM syndromes, appropriate diagnostic tests, and treatment regimens.
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Key Words
- ADR, adverse drug reactions
- AFB, acid fast bacilli
- AST, antimicrobial-susceptibility testing
- ATS, American Thoracic Society
- BCG, Bacille Calmette-Guerin
- CLSI, Clinical and Laboratory Standards Institute
- COPD, chronic obstructive pulmonary disease
- ECG, electrocardiogram
- EMB, ethambutol
- Erm, erythromycin ribosomal methylase
- FDA, Food and Drug Administration
- HIV, human immunodeficiency virus
- HRCT, high resolution computed tomography
- IDSA, Infectious Disease Society of America
- INF-γ, interferon- γ
- INH, isoniazid
- MAC, Mycobacterium avium complex
- MALDI-TOF, matrix-assisted laser desorption ionization time-of-flight mass spectrometry
- MGIT, mycobacteria growth indicator tube
- MIC, minimum inhibitory concentrations
- Mycobacterium abscessus
- Mycobacterium avium
- NTM, non-tuberculous mycobacteria
- Non-tuberculous mycobacteria
- PCR, polymerase chain reaction
- PFT, pulmonary function test
- TB, tuberculosis
- TDM, therapeutic drug monitoring
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Affiliation(s)
- Kelly M Pennington
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - Ann Vu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - Douglas Challener
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | | | - F N U Shweta
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - John D Zeuli
- Department of Pharmacy, Mayo Clinic Rochester, MN, USA
| | - Zelalem Temesgen
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
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Kong L, Xie B, Liu Q, Hua L, Bhusal A, Bao C, Hu J, Xu S. Application of acid-fast staining combined with GeneXpert MTB/RIF in the diagnosis of non-tuberculous mycobacteria pulmonary disease. Int J Infect Dis 2021; 104:711-717. [PMID: 33460835 DOI: 10.1016/j.ijid.2020.12.091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/25/2020] [Accepted: 12/30/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE To evaluate the clinical diagnostic value of positive acid-fast staining combined with negative GeneXpert MTB/RIF in the diagnosis of non-tuberculous mycobacteria pulmonary disease (NTM-PD). METHODS A total of 133 inpatients with confirmed NTM-PD were included consecutively between January 1, 2018 and December 31, 2019, at Tongji Hospital and Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, in Wuhan, China. One hundred patients with confirmed pulmonary tuberculosis (PTB) were randomly included as the control group. RESULTS The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of positive acid-fast staining combined with a negative GeneXpert MTB/RIF result were 51.13% (95% confidence interval (CI) 42.52-59.73%), 97.00% (95% CI 93.60-100.40%), 95.78% (95% CI 90.98-100.57%), and 59.88% (95% CI 52.25-67.51%), respectively. When subjects were limited to patients with positive acid-fast staining, the sensitivity of a negative GeneXpert MTB/RIF result was 88.31% (95% CI 80.97-95.65%). When acid-fast staining was conducted ≥3 times, the sensitivity of this combination diagnosis method increased to 61.67% (95% CI 49.00-74.33%). CONCLUSIONS Positive acid-fast staining combined with a negative GeneXpert MTB/RIF result could be an effective and time-saving method for the diagnosis of NTM-PD.
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Affiliation(s)
- Luxia Kong
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bangruan Xie
- Department of Tuberculosis and Infection, Wuhan Jinyintan Hospital, Wuhan, Hubei, China
| | - Qian Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lijuan Hua
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Anish Bhusal
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chen Bao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiannan Hu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuyun Xu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Peixoto ADS, Montenegro LML, Lima AS, Melo FL, Barbosa Júnior WL, Neves MMC, Ramos JP, Schindler HC, Medeiros ZM. Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting. Rev Soc Bras Med Trop 2020; 53:e20200211. [PMID: 33174954 PMCID: PMC7670742 DOI: 10.1590/0037-8682-0211-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION: Nontuberculous mycobacteria (NTM) species, as human pathogens,
are increasing in the world, as is the difficulty of accurately identifying
them. Differential diagnosis, especially between the M.
tuberculosis complex and NTM species, and the characterization
of NTM species is important. This study aimed to evaluate the performance of
a molecular system based on multiplex real-time PCR with high-resolution
melting (HRM) for the identification and differentiation of NTM species of
clinical importance of an endemic area for tuberculosis in northeastern
Brazil. METHODS: The technical protocol of the molecular system was based on multiplex
real-time PCR-HRM, and evaluated the sensitivity and specificity of the
detection of NTM species in mycobacterial clinical isolates from the studied
region. The gold standard method was specific gene sequencing. RESULTS: The sensitivity and specificity of multiplex real-time PCR-HRM modified for
differentiation between NTM and M. tuberculosis were 90%
and 100%, respectively. The PCR-HRM sensitivities for the characterization
of NTM species (M. kansasii, M. abscesses, M. avium, and M.
fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively.
CONCLUSIONS The multiplex real-time PCR-HRM modified assay has the potential to rapidly
and efficiently identify nontuberculous mycobacteria of clinical importance,
which is crucial for immediate implementation of the appropriate therapy and
thus avoiding complications and sequelae in patients.
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Affiliation(s)
- Aline Dos Santos Peixoto
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil.,Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil
| | | | - Andrea Santos Lima
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil
| | - Fábio Lopes Melo
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
| | | | | | - Jesus Pais Ramos
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Laboratório Nacional de Referência para Tuberculose, Rio de Janeiro, RJ, Brasil
| | | | - Zulma Maria Medeiros
- Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil.,Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
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26
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Feng JY, Chen WC, Chen YY, Su WJ. Clinical relevance and diagnosis of nontuberculous mycobacterial pulmonary disease in populations at risk. J Formos Med Assoc 2020; 119 Suppl 1:S23-S31. [PMID: 32482607 DOI: 10.1016/j.jfma.2020.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/26/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The lungs are the most common disease site of nontuberculous mycobacteria (NTM). However, the isolation of NTM in a respiratory specimen does not indicate lung disease (LD). Differentiation between NTM colonization and NTM-LD remains challenging. In this brief review, we summarize the clinical impact of NTM-LD on morbidity and mortality in high-risk populations. The diagnosis criteria for NTM-LD-including clinical features, radiological presentations, and microbiological evidence-are also reviewed, according to the latest American Thoracic Society (ATS)/Infectious Disease Society of America (IDSA) guideline and the British Thoracic Society (BTS) guideline. However, the diagnosis of NTM-LD does not necessitate the initiation of anti-NTM treatment. Both environmental, host, and bacterial factors should be considered to identify patients that require NTM-LD treatment.
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Affiliation(s)
- Jia-Yih Feng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Chih Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Ying Chen
- Department of Internal Medicine, Taipei Veterans General Hospital Taoyuan Branch, Taoyuan, Taiwan
| | - Wei-Juin Su
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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27
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The Quest for Systematic Epidemiology of Nontuberculous Mycobacterial Lung Disease in the United States: Closing in on an Elusive Goal. Ann Am Thorac Soc 2020; 17:169-172. [PMID: 32003606 DOI: 10.1513/annalsats.201911-846ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Shin S, Yoo IY, Shim HJ, Kang OK, Jhun BW, Koh WJ, Huh HJ, Lee NY. Diagnostic Performance of the GENEDIA MTB/NTM Detection Kit for Detecting Mycobacterium tuberculosis and Nontuberculous Mycobacteria With Sputum Specimens. Ann Lab Med 2020; 40:169-173. [PMID: 31650734 PMCID: PMC6822004 DOI: 10.3343/alm.2020.40.2.169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/29/2019] [Accepted: 09/25/2019] [Indexed: 01/02/2023] Open
Abstract
The GENEDIA MTB/NTM Detection Kit (GENEDIA MTB/NTM; Green Cross Medical Science Corp., Chungbuk, Korea) is a multiplex real-time PCR assay used for differential identification of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM). While the importance of differential identification of MTB/NTM is recognized, there is limited data on the performance of GENEDIA MTB/NTM assay to date. A total of 687 consecutive sputum specimens were cultured and analyzed with the GENEDIA MTB/NTM and GENEDIA MTB assays. Nineteen specimens (2.8%) were MTBC-positive, and 69 (10.0%) were NTM-positive based on mycobacterial culture. All specimens showed concordant results for MTBC using both assays, with a kappa value of 1.00, overall sensitivity of 63.2% (12/19), and specificity of 100% (668/668). The overall NTM sensitivity and specificity were 23.2% (16/69) and 99.7% (616/618) for GENEDIA MTB/NTM. The association between NTM-positivity using GENEDIA MTB/NTM and the diagnosis of NTM pulmonary disease was not statistically significant. In conclusion, the two real-time PCR assays showed similar diagnostic performance for MTBC detection. However, the sensitivity for NTM detection was lower than that for MTBC detection.
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Affiliation(s)
- Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - In Young Yoo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyang Jin Shim
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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29
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Bastian I, Shephard L, Lumb R. Revised guidelines for Australian laboratories performing mycobacteriology testing. ACTA ACUST UNITED AC 2020; 44. [PMID: 31940451 DOI: 10.33321/cdi.2020.44.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/27/2021] [Indexed: 11/20/2022]
Abstract
Mycobacteriology laboratories play a key role in tuberculosis (TB) control by providing phenotypic and molecular diagnostics, by performing molecular typing to aid contact tracing, and by supporting research and similar laboratories in Australia's neighbouring countries where TB is prevalent. The National Tuberculosis Advisory Committee (NTAC) published a set of laboratory guidelines in 2006 aiming to document the infrastructure, equipment, staffing and work practices required for safe high-quality work in Australian mycobacteriology laboratories. These revised guidelines have the same aims and have been through a similar extensive consultative peer-review process involving the Mycobacterium Reference Laboratory (MRL) network, the Mycobacterium Special Interest Group (SIG) of the Australian Society for Microbiology (ASM), and other relevant national bodies. This revised document contains several significant changes reflecting the publication of new biosafety guidelines and tuberculosis standards by various national and international organisations, technology developments - such as the MPT64-based immunochromatographic tests (ICTs) and the Xpert MTB/RIF assay, and updated work practices in mycobacteriology laboratories. The biosafety recommendations affirm the latest Australian/New Zealand Standard 2243.3: 2010 and promote a biorisk assessment approach that, in addition to the risk categorisation of the organism, also considers the characteristics of the procedure being performed. Using this biorisk assessment approach, limited manipulations, such as Ziehl-Neelsen (ZN) microscopy, MPT64 ICTs, and culture inactivation/DNA extraction for molecular testing, may be performed on a positive TB culture in a PC2 laboratory with additional features and work practices. Other significant changes include recommendations on the integration of MPT64 ICTs and novel molecular tests into TB laboratory workflows to provide rapid accurate results that improve the care of TB patients. This revised document supersedes the original 2006 publication. NTAC will periodically review these guidelines and provide updates as new laboratory technologies become available.
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Affiliation(s)
- Ivan Bastian
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Lisa Shephard
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
| | - Richard Lumb
- SA Pathology, PO Box 14, Rundle Mall, Adelaide SA 5000
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30
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Hasse B, Hannan MM, Keller PM, Maurer FP, Sommerstein R, Mertz D, Wagner D, Fernández-Hidalgo N, Nomura J, Manfrin V, Bettex D, Hernandez Conte A, Durante-Mangoni E, Tang THC, Stuart RL, Lundgren J, Gordon S, Jarashow MC, Schreiber PW, Niemann S, Kohl TA, Daley CL, Stewardson AJ, Whitener CJ, Perkins K, Plachouras D, Lamagni T, Chand M, Freiberger T, Zweifel S, Sander P, Schulthess B, Scriven JE, Sax H, van Ingen J, Mestres CA, Diekema D, Brown-Elliott BA, Wallace RJ, Baddour LM, Miro JM, Hoen B, Athan E, Bayer A, Barsic B, Corey GR, Chu VH, Durack DT, Fortes CQ, Fowler V, Hoen B, Krachmer AW, Durante-Magnoni E, Miro JM, Wilson WR. International Society of Cardiovascular Infectious Diseases Guidelines for the Diagnosis, Treatment and Prevention of Disseminated Mycobacterium chimaera Infection Following Cardiac Surgery with Cardiopulmonary Bypass. J Hosp Infect 2019; 104:214-235. [PMID: 31715282 DOI: 10.1016/j.jhin.2019.10.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/08/2019] [Indexed: 02/09/2023]
Abstract
Mycobacterial infection-related morbidity and mortality in patients following cardiopulmonary bypass surgery is high and there is a growing need for a consensus-based expert opinion to provide international guidance for diagnosing, preventing and treating in these patients. In this document the International Society for Cardiovascular Infectious Diseases (ISCVID) covers aspects of prevention (field of hospital epidemiology), clinical management (infectious disease specialists, cardiac surgeons, ophthalmologists, others), laboratory diagnostics (microbiologists, molecular diagnostics), device management (perfusionists, cardiac surgeons) and public health aspects.
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Affiliation(s)
- B Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland.
| | - M M Hannan
- Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - P M Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - F P Maurer
- Diagnostic Mycobacteriology Group, National and WHO Supranational Reference Center for Mycobacteria, Research Center, Borstel, Germany
| | - R Sommerstein
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - D Mertz
- Departments of Medicine, Health Research Methods, Evidence and Impact, and Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - D Wagner
- Department of Internal Medicine II, Division of Infectious Diseases, Medical Center - University of Freiburg, Freiburg i.Br, Germany
| | - N Fernández-Hidalgo
- Servei de Malalties Infeccioses, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Nomura
- Kaiser Permanente Infectious Diseases, Los Angeles Medical Center, CA, USA
| | - V Manfrin
- Infectious and Tropical Diseases Department, San Bortolo Hospital, Vincenca, Italy
| | - D Bettex
- Institute of Anesthesiology, University Hospital Zurich, Switzerland
| | - A Hernandez Conte
- Department of Anaesthesiology, Kaiser Permanente, Los Angeles Medical Center, CA, USA
| | - E Durante-Mangoni
- Infectious and Transplant Medicine, University of Campania 'L. Vanvitelli', Monaldi Hospital, Naples, Italy
| | - T H-C Tang
- Division of Infectious Diseases, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - R L Stuart
- Monash Infectious Diseases, Monash Health, Australia
| | - J Lundgren
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - S Gordon
- Department of Infectious Diseases, Cleveland Clinic, OH, USA
| | - M C Jarashow
- Acute Communicable Disease Control, Los Angeles Department of Public Health, LA, USA
| | - P W Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland
| | - S Niemann
- Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany and German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Borstel, Germany
| | - T A Kohl
- Molecular and Experimental Mycobacteriology Group, Research Center Borstel, Borstel, Germany and German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Borstel, Germany
| | - C L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, CO, USA
| | - A J Stewardson
- Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, Australia
| | - C J Whitener
- Penn State Health, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - K Perkins
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - D Plachouras
- Healthcare-associated Infections, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - T Lamagni
- National Infection Service, Public Health England, London, UK
| | - M Chand
- National Infection Service, Public Health England, London, UK; Guy's and St Thomas' NHS Foundation Trust, Imperial College London, UK
| | - T Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - S Zweifel
- Ophthalmology Unit, University of Zurich, Switzerland
| | - P Sander
- National Center for Mycobacteria, Zurich, Switzerland, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - B Schulthess
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - J E Scriven
- Department of Infection and Tropical Medicine, University Hospitals Birmingham, Birmingham, UK
| | - H Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Zurich, Switzerland
| | - J van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - C A Mestres
- Clinic for Cardiovascular Surgery, University Hospital and University of Zurich, Switzerland
| | - D Diekema
- Division of Infectious Diseases, University of Iowa, Carver College of Medicine, IA, USA
| | - B A Brown-Elliott
- Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - R J Wallace
- Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - L M Baddour
- Division of Infectious Diseases, Departments of Medicine and Cardiovascular Diseases, Mayo Clinic, College of Medicine and Science, Rochester, MN, USA
| | - J M Miro
- Infectious Diseases Service at the Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - B Hoen
- Department of Infectious Diseases and Tropical Medicine, University Medical Center of Nancy, Vandoeuvre Cedex, France.
| | | | | | - E Athan
- Infectious Diseases Department at Barwon Health, University of Melbourne and Deakin University, Australia
| | - A Bayer
- Geffen School of Medicine at UCLA Senior Investigator - LA Biomedical Research Institute at Harbor-UCLA, USA
| | - B Barsic
- Department for Infectious Diseases, School of Medicine, University of Zagreb, Croatia
| | - G R Corey
- Duke University Medical Center, Hubert-Yeargan Center for Global Health, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - V H Chu
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - D T Durack
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - C Q Fortes
- Division of Infectious Diseases, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - V Fowler
- Departments of Medicine and Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - B Hoen
- Department of Infectious Diseases and Tropical Medicine, University Medical Center of Nancy, Vandoeuvre Cedex, France
| | - A W Krachmer
- Harvard Medical School, Division of Infectious Diseases at the Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - E Durante-Magnoni
- Infectious and Transplant Medicine of the 'V. Monaldi' Teaching Hospital in Naples, University of Campania 'L. Vanvitelli', Italy
| | - J M Miro
- Infectious Diseases at the Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - W R Wilson
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, College of Medicine and Science, Rochester, MN, USA
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GenoType NTM-DR Performance Evaluation for Identification of Mycobacterium avium Complex and Mycobacterium abscessus and Determination of Clarithromycin and Amikacin Resistance. J Clin Microbiol 2019; 57:JCM.00516-19. [PMID: 31167842 DOI: 10.1128/jcm.00516-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
We evaluated the GenoType NTM-DR (NTM-DR) line probe assay for identifying Mycobacterium avium complex (MAC) species and Mycobacterium abscessus subspecies and for determining clarithromycin and amikacin resistance. Thirty-eight reference strains and 145 clinical isolates (58 MAC and 87 M. abscessus isolates), including 54 clarithromycin- and/or amikacin-resistant strains, were involved. The performance of the NTM-DR assay in rapid identification was evaluated by comparison with results of multigene sequence-based typing, whereas performance in rapid detection of clarithromycin and amikacin resistance was evaluated by comparison with sequencing of the erm(41), rrl, and rrs genes and drug susceptibility testing (DST). The accuracies of MAC and M. abscessus (sub)species identification were 92.1% (35/38) and 100% (145/145) for the 38 reference strains and 145 clinical isolates, respectively. Three MAC strains other than M. intracellulare were found to cross-react with the M. intracellulare probe in the assay. Regarding clarithromycin resistance, NTM-DR detected rrl mutations in 52 isolates and yielded 99.3% (144/145) and 98.6% (143/145) concordant results with sequencing and DST, respectively. NTM-DR sensitivity and specificity in the detection of clarithromycin resistance were 96.3% (52/54) and 100% (91/91), respectively. The NTM-DR yielded accurate erm(41) genotype results for all 87 M. abscessus isolates. Regarding amikacin resistance, NTM-DR detected rrs mutations in five isolates and yielded 99.3% (144/145) and 97.9% (142/145) concordant results with sequencing and DST, respectively. Our results indicate that the NTM-DR assay is a straightforward and accurate approach for discriminating MAC and M. abscessus (sub)species and for detecting clarithromycin and amikacin resistance mutations and that it is a useful tool in the clinical setting.
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32
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Cowman S, van Ingen J, Griffith DE, Loebinger MR. Non-tuberculous mycobacterial pulmonary disease. Eur Respir J 2019; 54:13993003.00250-2019. [PMID: 31221809 DOI: 10.1183/13993003.00250-2019] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 02/03/2023]
Abstract
Nontuberculous mycobacterial pulmonary disease (NTM-PD) is a challenging infection which is becoming increasingly prevalent, particularly in the elderly, for reasons which are unknown. While underlying lung disease is a well-established risk factor for NTM-PD, it may also occur in apparently healthy individuals. No single common genetic or immunological defect has been identified in this group, and it is likely that multiple pathways contribute towards host susceptibility to NTM-PD which further interact with environmental and microbiological factors leading to the development of disease.The diagnosis of NTM-PD relies on the integration of clinical, radiological and microbiological results. The clinical course of NTM-PD is heterogeneous, with some patients remaining stable without the need for treatment and others developing refractory disease associated with considerable mortality and morbidity. Treatment regimens are based on the identity of the isolated species, drug sensitivity testing (for some agents) and the severity of disease. Multiple antibiotics are typically required for prolonged periods of time and treatment is frequently poorly tolerated. Surgery may be beneficial in selected cases. In some circumstances cure may not be attainable and there is a pressing need for better regimens to treat refractory and drug-resistant NTM-PD.This review summarises current knowledge on the epidemiology, aetiology and diagnosis of NTM-PD and discusses the treatment of two of the most clinically significant species, the M. avium and M. abscessus complexes, with a focus on refractory disease and novel therapies.
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Affiliation(s)
- Steven Cowman
- Host Defence Unit, Royal Brompton Hospital, London, UK.,Imperial College, London, UK
| | - Jakko van Ingen
- Dept of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David E Griffith
- Dept of Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Michael R Loebinger
- Host Defence Unit, Royal Brompton Hospital, London, UK .,Imperial College, London, UK
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33
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van den Broek T, Janssen NG, Hetem DJ, Bekers W, Kamst M, Fluit AC, van Ingen J, Kusters JG, Rentenaar RJ. INNO-LiPA DNA line probe assay misidentification of M. smegmatis as Mycobacterium fortuitum complex. Diagn Microbiol Infect Dis 2019; 95:114858. [PMID: 31358343 DOI: 10.1016/j.diagmicrobio.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/26/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Seven weeks after being kicked in the face by a cow, a 34-year-old male patient developed a posttraumatic mycobacterial lymphadenitis. A rapidly growing mycobacterial isolate cultured from a surgically drained lymphadenitis pus specimen was identified as Mycobacterium smegmatis by matrix-assisted laser desorption/ionization mass spectrometry and a combination of ITS-, hsp65-, and 16S rRNA-DNA sequence analysis, but as Mycobacterium fortuitum complex using the commercial INNO-LiPA Mycobacteria v2 line probe assay. As it is unclear if the misidentification of this strain is an exception, more research is required.
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Affiliation(s)
- Theo van den Broek
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands.
| | - Nard G Janssen
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - David J Hetem
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands; Department of Medical Microbiology, Haaglanden Medical Center, 2501, CK, The Hague, The Netherlands
| | - Wouter Bekers
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Miranda Kamst
- National Institute for Public Health and the Environment (RIVM), 3720, BA, Bilthoven, The Netherlands
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, 6500, HB, Nijmegen, The Netherlands
| | - Johannes G Kusters
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
| | - Rob J Rentenaar
- Department of Medical Microbiology, University Medical Center Utrecht, 3508, GA, Utrecht, The Netherlands
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34
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Fang H, Shangguan Y, Wang H, Ji Z, Shao J, Zhao R, Wang S, Zheng L, Jin X, Huang S, Xu K, Sheng J. Multicenter evaluation of the biochip assay for rapid detection of mycobacterial isolates in smear-positive specimens. Int J Infect Dis 2019; 81:46-51. [PMID: 30685589 DOI: 10.1016/j.ijid.2019.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/13/2019] [Accepted: 01/19/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES The objective of this study was to conduct a multicentre evaluation of the performance of the biochip assay in the rapid identification of mycobacteria in smear-positive sputum specimens. METHODS A total of 1751 sputum specimens were obtained from 7 cities in Zhejiang, China. All of the specimens were used for the discrimination of Mycobacterium species using the biochip assay, and the results were compared to the golden standard method of culture, hsp65, 16S rRNA and rpoB sequence analysis. RESULTS In the 1751 sputum specimens, 1685 samples were cultured successfully; among these samples, 1361 were Mycobacterium tuberculosis, 323 were NTM and 1 was Nocadia farcinica. Of the 323 NTM, most of them were Mycobacterium intracellulare(52.5%) followed by Mycobacterium abscessus (20.7%), Mycobacterium avium (11.7%), Mycobacterium kansasii (9.6%) and Mycobacterium fortuitum (1.9%). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the biochip assay to differentiate TB and NTM from AFB positive specimens were 99.8%, 99.7%, 99.9%, 99.1%, 98.8%, 1, 1, and 99.7%, respectively. The concordance between the biochip assay and mycobacterial culture for the identification of NTM species was 95.4%. CONCLUSIONS The biochip assay is a reliable tool for the rapid identification of most mycobacteria in clinical sputum specimens. This assay can be helpful for physicians in the early diagnosis and treatment of mycobacterium infections.
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Affiliation(s)
- Hong Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Yanwan Shangguan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Hao Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Jundan Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Ruihong Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Shuting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Lin Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Xiuyuan Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Shujuan Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China.
| | - Jifang Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang, China.
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Abstract
Nontuberculous mycobacteria (NTM) are important emerging cystic fibrosis (CF) pathogens, with estimates of prevalence ranging from 6% to 13%. Diagnosis of NTM disease in patients with CF is challenging, as the infection may remain indolent in some, without evidence of clinical consequence, whereas other patients suffer significant morbidity and mortality. Treatment requires prolonged periods of multiple drugs and varies depending on NTM species, resistance pattern, and extent of disease. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in CF patients is a research priority, as a lifelong strategy is needed for this high-risk population.
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Affiliation(s)
- Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Denver School of Medicine, 13123 East 16th Avenue, Box B-395, Aurora, CO 80045, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO 80045, USA.
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36
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Mycobacterium avium: an overview. Tuberculosis (Edinb) 2019; 114:127-134. [PMID: 30711152 DOI: 10.1016/j.tube.2018.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 12/20/2018] [Accepted: 12/28/2018] [Indexed: 01/15/2023]
Abstract
Mycobacterium avium is an environmental microorganism found in soil and water sources worldwide. It is the most prevalent species of nontuberculous mycobacteria that causes infectious diseases, especially in immunocompromised individuals. This review discusses and highlights key topics about M. avium, such as epidemiology, pathogenicity, glycopeptidolipids, laboratory identification, genotyping, antimicrobial therapy and antimicrobial resistance. Additionally, the main comorbidities associated with M. avium infection are discussed.
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37
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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._.
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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
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38
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Mycobacterium avium complex bacteria remain viable in sputum during storage and refrigeration. Diagn Microbiol Infect Dis 2018; 92:309-310. [DOI: 10.1016/j.diagmicrobio.2018.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/12/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022]
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39
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Zweijpfenning S, Hoefsloot W, van Ingen J. Nontuberculous mycobacteria. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10022717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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40
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Ravnholt C, Kolpen M, Skov M, Moser C, Katzenstein TL, Pressler T, Høiby N, Qvist T. The importance of early diagnosis of Mycobacterium abscessus complex in patients with cystic fibrosis. APMIS 2018; 126:885-891. [PMID: 30456869 DOI: 10.1111/apm.12903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/09/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterium abscessus complex can cause severe lung infections and has proven to be a serious threat to patients with cystic fibrosis and a challenge for clinicians due to difficulties in timely diagnosis and complex multidrug treatment regimes. Mycobacterial culture is the gold standard for diagnosis, but in most cystic fibrosis centers it is performed less frequently than culture for other pathogens. Consensus today recommends just one annual mycobacterial culture for asymptomatic patients with cystic fibrosis, a strategy likely to lead to diagnostic delays. Postponement of diagnosis might be the deciding factor in whether an early colonization turns into chronic infection. This review highlights the latest developments in knowledge about the pathogenicity and clinical consequences of M. abscessus complex pulmonary disease, addressing the central theme of why pulmonary infection requires early identification and aggressive antibiotic treatment. The window of opportunity, before M. abscessus complex transforms from a mucosal colonizer to a chronic biofilm infection, is where microbial eradication is most likely to be successful, making early diagnosis essential for improved outcomes.
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Affiliation(s)
- Cecilie Ravnholt
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Mette Kolpen
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Skov
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark
| | - Claus Moser
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Terese L Katzenstein
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Tania Pressler
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Institute of Immunology and Medical Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tavs Qvist
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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41
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Dakić I, Arandjelović I, Savić B, Jovanović S, Tošić M, Kurucin T, Vuković D. Pulmonary isolation and clinical relevance of nontuberculous mycobacteria during nationwide survey in Serbia, 2010-2015. PLoS One 2018; 13:e0207751. [PMID: 30462740 PMCID: PMC6248987 DOI: 10.1371/journal.pone.0207751] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/06/2018] [Indexed: 11/19/2022] Open
Abstract
The rates of pulmonary colonization and disease due to nontuberculous mycobacteria (NTM) appear to be increasing globally, but diversity of species recovered as well as clinical relevance of NTM isolates differ considerably by geographic region. The first nationwide study of isolation frequency and clinical significance of NTM in Serbia included all patients with respiratory specimens yielding a positive NTM culture over the six-year period, 2010–2015. We analyzed trends in annual NTM isolation and NTM pulmonary disease (PD) incidence rates, with NTM PD cases defined in accordance with microbiological criteria established by the American Thoracic Society/Infectious Diseases Society of America (ATS/IDSA). 777 pulmonary NTM isolates were collected from 565 patients, of whom 126 (22.3%) met the ATS/IDSA criteria. The annual NTM isolation and NTM PD incidence rates per 100,000 changed over 2010–2015 from 0.9 to 1.6 (p = 0.1746) and from 0.18 to 0.48 (p = f0.0040), respectively. Both isolation and disease rates increased considerably with age, while higher NTM PD rates were also associated with residence in urbanized areas. Diversity of NTM species isolated was shown to be region-specific, with M. xenopi as the most prevalent species (17.3%), and increasing isolation rates of rapid growing mycobacteria (RGM) (p = 0.0072). M. xenopi was also the most common cause of NTM PD (28.6%), followed by RGM (27.8%). With 73% clinically relevant isolates, M. abscessus was identified as the most clinically relevant NTM species. While NTM PD obviously remains a rare disease in Serbia, the overall results justify recognition of NTM as pathogens of rising importance, and require further characterization of their epidemiology in the country.
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Affiliation(s)
- Ivana Dakić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Irena Arandjelović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Branislava Savić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Snežana Jovanović
- Department of Microbiology, Clinical Center of Serbia, Belgrade, Serbia
| | - Mirjana Tošić
- Department of Microbiology, Municipal Institute for Pulmonary Diseases and Tuberculosis, Belgrade, Serbia
| | - Tatjana Kurucin
- Center for Microbiology, Virology and Immunology, Institute for Pulmonary Diseases of Vojvodina, Sremska Kamenica, Serbia
| | - Dragana Vuković
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- * E-mail:
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42
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Vinnard C, Mezochow A, Oakland H, Klingsberg R, Hansen-Flaschen J, Hamilton K. Assessing Response to Therapy for Nontuberculous Mycobacterial Lung Disease: Quo Vadis? Front Microbiol 2018; 9:2813. [PMID: 30524407 PMCID: PMC6256187 DOI: 10.3389/fmicb.2018.02813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/01/2018] [Indexed: 12/26/2022] Open
Abstract
Assessing progression of disease or response to treatment remains a major challenge in the clinical management of nontuberculous mycobacterial (NTM) infections of the lungs. Serial assessments of validated measures of treatment response address whether the current therapeutic approach is on track toward clinical cure, which remains a fundamental question for clinicians and patients during the course of NTM disease treatment. The 2015 NTM Research Consortium Workshop, which included a patient advisory panel, identified treatment response biomarkers as a priority area for investigation. Limited progress in addressing this challenge also hampers drug development efforts. The Biomarker Qualification Program at the FDA supports the use of a validated treatment response biomarker across multiple drug development programs. Current approaches in clinical practice include microbiologic and radiographic monitoring, along with symptomatic and quality-of-life assessments. Blood-based monitoring, including assessments of humoral and cell-mediated NTM-driven immune responses, remain under investigation. Alignment of data collection schemes in prospective multicenter studies, including the support of biosample repositories, will support identification of treatment response biomarkers under standard-of-care and investigational therapeutic strategies. In this review, we outline the role of treatment monitoring biomarkers in both clinical practice and drug development frameworks.
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Affiliation(s)
- Christopher Vinnard
- Public Health Research Institute, New Jersey Medical School, Newark, NJ, United States
| | - Alyssa Mezochow
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hannah Oakland
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Ross Klingsberg
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - John Hansen-Flaschen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Keith Hamilton
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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43
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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44
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Shteinberg M, Stein N, Adir Y, Ken-Dror S, Shitrit D, Bendayan D, Fuks L, Saliba W. Prevalence, risk factors and prognosis of nontuberculous mycobacterial infection among people with bronchiectasis: a population survey. Eur Respir J 2018; 51:13993003.02469-2017. [PMID: 29545278 DOI: 10.1183/13993003.02469-2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Michal Shteinberg
- Pulmonology Institute, Carmel Medical Center, Haifa, Israel.,CF Center, Carmel Medical Center, Haifa, Israel.,Technion - Israel Institute of Technology, B. Rappaport Faculty of Medicine, Haifa, Israel
| | - Nili Stein
- Technion - Israel Institute of Technology, B. Rappaport Faculty of Medicine, Haifa, Israel.,Dept of Community Medicine and Epidemiology, Carmel Medical Center, Clalit Health Services, Haifa, Israel
| | - Yochai Adir
- Pulmonology Institute, Carmel Medical Center, Haifa, Israel.,Technion - Israel Institute of Technology, B. Rappaport Faculty of Medicine, Haifa, Israel
| | - Shifra Ken-Dror
- Microbiology Laboratory, Haifa and Western Gallilee, Clalit Health Services, Haifa, Israel
| | - David Shitrit
- Pulmonology Dept, Meir Medical Center, Kfar Sava, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Bendayan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pulmonary and Tuberculosis Dept, Shmuel Harofe Hospital, Be'er Ya'akov, Israel
| | - Leonardo Fuks
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pulmonary Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Walid Saliba
- Technion - Israel Institute of Technology, B. Rappaport Faculty of Medicine, Haifa, Israel.,Dept of Community Medicine and Epidemiology, Carmel Medical Center, Clalit Health Services, Haifa, Israel
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45
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Haworth CS, Banks J, Capstick T, Fisher AJ, Gorsuch T, Laurenson IF, Leitch A, Loebinger MR, Milburn HJ, Nightingale M, Ormerod P, Shingadia D, Smith D, Whitehead N, Wilson R, Floto RA. British Thoracic Society guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). Thorax 2017; 72:ii1-ii64. [DOI: 10.1136/thoraxjnl-2017-210927] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 01/18/2023]
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46
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[Nontuberculous mycobacteria in sputum : Recommendations for diagnosis and treatment]. Internist (Berl) 2017; 58:1163-1170. [PMID: 29038903 DOI: 10.1007/s00108-017-0330-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pulmonary diseases caused by nontuberculous mycobacteria (NTM) have increased over the last years and decades in Germany and also worldwide. Because the disease is more frequent in patients with immunodeficiencies and chronic respiratory diseases, e.g. bronchiectasis, advanced chronic obstructive lung disease (COPD) and cystic fibrosis (CF), an infection with mycobacteria should always be considered in this patient group. The detection in sputum alone is not an indication for treatment but the correct diagnosis should be based on the appropriate clinical symptoms as well as radiological and microbiological criteria. The diagnosis is often delayed because the symptoms are unspecific. The treatment of pulmonary NTM disease is difficult and tedious and for these reasons is often prematurely terminated. Adherence of treating physicians to the guidelines is also conspicuously low. Before starting treatment, it is important to carefully define the goals and clarify the risks and benefits of the treatment with the patient. As adverse toxic events can occur during treatment, it should be closely monitored. In the case of an infrequent pathogen or a severe course of the disease, referral to an NTM specialist center should be undertaken.
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47
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Ebeh Messanga R, Dominique Serge NB, Abouem A. Zintchem A, Norbert MNII, Esther Del Florence MN, Patrick Hervé BD, Maximilienne Ascension N, Alex De Théodore A, Dieudonné Emmanuel P, Christian G. B, Koert U. Rauvolfianine, a new antimycobacterial glyceroglycolipid and other constituents from Rauvolfia caffra. Sond (Apocynaceae). Nat Prod Res 2017; 32:1971-1976. [DOI: 10.1080/14786419.2017.1356832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Robert Ebeh Messanga
- Faculty of Science, Department of Organic Chemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Ngono Bikobo Dominique Serge
- Faculty of Science, Department of Organic Chemistry, University of Yaoundé I, Yaoundé, Cameroon
- Department Chemie, Universität Fribourg, Fribourg, Switzerland
| | - Auguste Abouem A. Zintchem
- Faculty of Science, Department of Organic Chemistry, University of Yaoundé I, Yaoundé, Cameroon
- Department of Chemistry, Higher Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - Mbabi Nyemeck II Norbert
- Faculty of Science, Department of Organic Chemistry, University of Yaoundé I, Yaoundé, Cameroon
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | | | | | | | | | | | | | - Ulrich Koert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
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48
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Abstract
Nontuberculous mycobacteria (NTM) are emerging pathogens that affect both immunocompromised and immunocompetent patients. The development of molecular methods has allowed the characterization of new species and the identification of NTM to the precise species and subspecies levels. The incidence and prevalence of NTM lung disease are increasing worldwide, and this syndrome accounts for the majority of clinical cases of NTM disease. Common causative organisms of pulmonary infection are the slowly growing mycobacteria Mycobacterium avium complex and Mycobacterium kansasii and the rapidly growing mycobacteria, including Mycobacterium abscessus complex. NTM lung disease often affects elderly people with chronic lung disease and may be a manifestation of a complex genetic disorder determined by interactions among multiple genes, as well as environmental exposures. To be diagnosed with NTM lung disease, patients should meet all clinical and microbiologic criteria, but the decision to start treatment is complex, requiring careful individualized analysis of risks and benefits. Clinicians should be alert to the unique aspects of NTM lung disease, including the need for proper diagnosis, the availability of advanced molecular methods for species and subspecies identification, and the benefits and limitations of recommended treatments.
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49
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Abstract
Despite the ubiqitous nature of Mycobacterium avium complex (MAC) organisms in the environment, relatively few of those who are infected develop disease. Thus, some degree of susceptibility due to either underlying lung disease or immunosuppression is required. The frequency of pulmonary MAC disease is increasing in many areas, and the exact reasons are unknown. Isolation of MAC from a respiratory specimen does not necessarily mean that treatment is required, as the decision to treatment requires the synthesis of clinical, radiographic, and microbiologic information as well as a weighing of the risks and benefits for the individual patient. Successful treatment requires a multipronged approach that includes antibiotics, aggressive pulmonary hygiene, and sometimes resection of the diseased lung. A combination of azithromycin, rifampin, and ethambutol administered three times weekly is recommend for nodular bronchiectatic disease, whereas the same regimen may be used for cavitary disease but administered daily and often with inclusion of a parenteral aminoglycoside. Disseminated MAC (DMAC) is almost exclusively seen in patients with late-stage AIDS and can be treated with a macrolide in combination with ethambutol, with or without rifabutin: the most important intervention in this setting is to gain HIV control with the use of potent antiretroviral therapy. Treatment outcomes for many patients with MAC disease remain suboptimal, so new drugs and treatment regimens are greatly needed. Given the high rate of reinfection after cure, one of the greatest needs is a better understanding of where infection occurs and how this can be prevented.
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50
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Kušar D, Zajc U, Jenčič V, Ocepek M, Higgins J, Žolnir-Dovč M, Pate M. Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish. JOURNAL OF FISH DISEASES 2017; 40:773-784. [PMID: 27747884 DOI: 10.1111/jfd.12558] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Fish are commonly infected with non-tuberculous mycobacteria (NTM), which should be regarded as potential pathogens when handling aquarium fish and equipment. This study examined 107 aquarium fish from pet shops. Cultivation of the fish samples using different selective media was conducted for identification of NTM. Isolates were identified using the GenoType Mycobacterium common mycobacteria and additional species assays, sequencing of the 16S rRNA and rpoB genes, and real-time PCR assay for identification of Mycobacterium (M.) marinum. Among the investigated fish, 79.4% (85/107) were positive for mycobacteria, with 8.2% (7 of 85) having two mycobacterial species present. Among the positive fish, the common pathogens M. marinum, Mycobacterium fortuitum (M. fortuitum group) and Mycobacterium chelonae were identified in approx. 90% of fish and other NTM species in 10%, including Mycobacterium peregrinum/septicum, Mycobacterium gordonae, Mycobacterium arupense, Mycobacterium kansasii, Mycobacterium ulcerans and Mycobacterium setense. The well-known human pathogen M. marinum was present in 10.6% of the positive fish (9 of 85). The species of mycobacteria identified in the study are not only recognized as aquarium fish pathogens, but can also cause pathology in humans. Microbiological and clinical communities should therefore be sensitized to the role of NTM in infections associated with exposure to aquarium fish.
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Affiliation(s)
- D Kušar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - U Zajc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - V Jenčič
- Veterinary Faculty, Institute of Pathology, Wild Animals, Fish and Bees, University of Ljubljana, Ljubljana, Slovenia
| | - M Ocepek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - J Higgins
- Mycobacteria and Brucella Section, National Veterinary Services Laboratories, United States Department of Agriculture - Animal and Plant Health Inspection Service (USDA-APHIS), Ames, IA, USA
| | - M Žolnir-Dovč
- National Reference Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - M Pate
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
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