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Anh NK, Phat NK, Thu NQ, Tien NTN, Eunsu C, Kim HS, Nguyen DN, Kim DH, Long NP, Oh JY. Discovery of urinary biosignatures for tuberculosis and nontuberculous mycobacteria classification using metabolomics and machine learning. Sci Rep 2024; 14:15312. [PMID: 38961191 PMCID: PMC11222504 DOI: 10.1038/s41598-024-66113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) infection diagnosis remains a challenge due to its overlapping clinical symptoms with tuberculosis (TB), leading to inappropriate treatment. Herein, we employed noninvasive metabolic phenotyping coupled with comprehensive statistical modeling to discover potential biomarkers for the differential diagnosis of NTM infection versus TB. Urine samples from 19 NTM and 35 TB patients were collected, and untargeted metabolomics was performed using rapid liquid chromatography-mass spectrometry. The urine metabolome was analyzed using a combination of univariate and multivariate statistical approaches, incorporating machine learning. Univariate analysis revealed significant alterations in amino acids, especially tryptophan metabolism, in NTM infection compared to TB. Specifically, NTM infection was associated with upregulated levels of methionine but downregulated levels of glutarate, valine, 3-hydroxyanthranilate, and tryptophan. Five machine learning models were used to classify NTM and TB. Notably, the random forest model demonstrated excellent performance [area under the receiver operating characteristic (ROC) curve greater than 0.8] in distinguishing NTM from TB. Six potential biomarkers for NTM infection diagnosis, including methionine, valine, glutarate, 3-hydroxyanthranilate, corticosterone, and indole-3-carboxyaldehyde, were revealed from univariate ROC analysis and machine learning models. Altogether, our study suggested new noninvasive biomarkers and laid a foundation for applying machine learning to NTM differential diagnosis.
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Affiliation(s)
- Nguyen Ky Anh
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Quang Thu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Tran Nam Tien
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Cho Eunsu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Ho-Sook Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Duc Ninh Nguyen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.
| | - Jee Youn Oh
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, 08308, Republic of Korea.
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Xie L, Zhu XY, Xu L, Xu XX, Ruan ZF, Huang MX, Chen L, Jiang XW. Accurate and affordable detection of rifampicin and isoniazid resistance in Tuberculosis sputum specimens by multiplex PCR-multiple probes melting analysis. Infection 2024:10.1007/s15010-024-02295-w. [PMID: 38884858 DOI: 10.1007/s15010-024-02295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/10/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Escalating cases of multidrug-resistant tuberculosis (MDR-TB) pose a major challenge to global TB control efforts, necessitating innovative diagnostics to empower decentralized detection of gene mutations associated with resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis (M. tuberculosis) in resource-constrained settings. METHODS Combining multiplex fluorescent PCR and Multiple Probes Melting Analysis, we identified mutations in the rpoB, katG, ahpC and inhA genes from sputum specimens. We first constructed a reference plasmid library comprising 40 prevalent mutations in the target genes' resistance determining regions and promoters, serving as positive controls. Our assay utilizes a four-tube asymmetric PCR method with specifically designed molecular beacon probes, enabling simultaneous detection of all 40 mutations. We evaluated the assay's effectiveness using DNA isolated from 50 clinically confirmed M. tuberculosis sputum specimens, comparing our results with those obtained from Sanger sequencing and retrospective validation involving bacteriological culture and phenotypic drug susceptibility testing (pDST). We also included the commercial Xpert MTB/RIF assay for accuracy comparison. RESULTS Our data demonstrated remarkable sensitivity in detecting resistance to RIF and INH, achieving values of 93.33% and 95.24%, respectively, with a specificity of 100%. The concordance between our assay and pDST was 98.00%. Furthermore, the accuracy of our assay was comparable to both Sanger sequencing and the Xpert assay. Importantly, our assay boasts a 4.2-h turnaround time and costs only $10 per test, making it an optimal choice for peripheral healthcare settings. CONCLUSION These findings highlight our assay's potential as a promising tool for rapidly, accurately, and affordably detecting MDR-TB.
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Affiliation(s)
- Long Xie
- Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Xiao-Ya Zhu
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Li Xu
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Xiao-Xie Xu
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Ze-Fan Ruan
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Ming-Xiang Huang
- Fuzhou Pulmonary Hospital and Fujian Medical University Clinical Teaching Hospital, Fuzhou, China.
| | - Li Chen
- Chaoshan Hospital, The First Affiliated Hospital of Jinan University, Chaozhou, China.
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Xi-Wen Jiang
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China.
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China.
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China.
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3
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Pedlar M, Emery MJ, Warburton PJ. Amplifying PCR productivity and environmental sustainability through shortened cycling protocols. Biochimie 2024; 221:60-64. [PMID: 38262587 DOI: 10.1016/j.biochi.2024.01.013] [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: 06/24/2023] [Revised: 01/06/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Since its inception in the 1980s, advancements in PCR technology using improved thermal cyclers, engineered DNA polymerases and commercial master mixes, have led to increased PCR productivity. Despite these advancements, PCR cycling protocols have largely remained unchanged over the same period. This study aimed to systemically evaluate the effect of reduced PCR cycling parameters on amplicon production. The 1466bp fragment from the 16S rRNA gene present in low-, medium- and high-CG bacteria was amplified using three commercially available PCR master mixes. The shortest cycling parameters required to successfully amplify the 16S fragment from all bacteria and master mixes comprised 30-cycles of 5 s denaturation, 25 s annealing, and 25 s extension. While all produced an amplicon with sufficient yield to enable downstream sequence analysis, the PCRBIO Ultra Mix in conjunction with the shortened parameters was found to achieve the highest amplicon yield across low-, medium- and high CG bacteria. Comparing the run times to that of a typical 16S PCR protocol, the shortened cycling parameters reduced the program duration by 46 % and consumed 50 % less electricity, translating into increased productivity and helping to improve laboratory environmental sustainability.
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Affiliation(s)
- Matthew Pedlar
- School of Biomedical Sciences, University of Plymouth, PL4 8AA, UK
| | - Matthew J Emery
- School of Biological and Marine Sciences, University of Plymouth, PL4 8AA, UK
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Chang LK, Wang PH, Lee TF, Huang YT, Shu CC, Wang HC, Yu CJ. Microbiological persistence in patients with Mycobacterium abscessus complex lung disease: The prevalence, predictors, and the impact on progression. Int J Infect Dis 2024; 139:118-123. [PMID: 37977501 DOI: 10.1016/j.ijid.2023.11.018] [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: 06/29/2023] [Revised: 10/26/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVES Persistent growth of Mycobacterium abscessus complex (MABC) in the respiratory system is not uncommon and may indicate continuous infection of MABC lung disease (MABC-LD), but its prevalence, risk factors, and clinical impact have not been investigated. METHODS The present study was conducted in two medical centers in northern Taiwan. We enrolled patients with MABC-LD and investigated the prevalence and predictors of persistent culture positivity (MABC-PP). Furthermore, we analyzed the association between MABC-PP and radiographic or clinical progression. RESULTS Among 189 patients with MABC-LD, 58 were in the MABC-PP group. Independent predictors for MABC-PP included an increasing radiographic score and highest acid-fast stain (AFS) of strong positivity (3-4+) at initial diagnosis (compared with negative AFS). MABC-PP and highest AFS were independently associated with MABC-LD progression by the multivariable analysis model. The adjusted hazard ratio increased to 3.56 when the two independent factors existed. CONCLUSIONS MABC-PP accounted for 30.7% and was predicted by initial AFS grade and radiographic score. Patients with MABC-PP, and highest AFS grade might have disease progression.
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Affiliation(s)
- Ling-Kai Chang
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch BioMedical Park Hospital, Zhubei City, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ping-Huai Wang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chin-Chung Shu
- College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Hao-Chien Wang
- College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch BioMedical Park Hospital, Zhubei City, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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5
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Costa M, Caria JP, Caiano JB, Caeiro A, Maltez F. Tuberculous Meningitis: An Endemic Cause of Intracranial Hypertension. Cureus 2024; 16:e51532. [PMID: 38304681 PMCID: PMC10831199 DOI: 10.7759/cureus.51532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
Tuberculous meningitis (TBM) presents a complex clinical scenario, often marked by delayed recognition and high mortality. Our case involves a 27-year-old woman from Nepal with no significant medical history, presented with a two-week history of fatigue, altered consciousness, dizziness, vomiting, fever, holocranial headache, and photophobia. Initial examination revealed signs consistent with meningitis, including fever, hypertensive state, prostration, bilateral exophthalmos, sixth cranial nerve paresis, and positive Kernig/Brudzinski signs. Cerebrospinal fluid (CSF) exhibited characteristics typical of TBM: turbidity, lymphocytic-predominant pleocytosis, low glucose, and elevated protein. The patient was promptly started on meningeal doses of vancomycin, ceftriaxone, and acyclovir. However, persistent fever, neurological deterioration, and signs of increased intracranial pressure led to the decision to initiate conventional empiric treatment of tuberculosis (TB) with isoniazid, rifampicin, pyrazinamide, and ethambutol (HRZE) and dexamethasone 1 week before cultural positivity for Mycobacterium tuberculosis of CSF. The case underscores the importance of considering TBM in patients from endemic regions, interpreting CSF findings, and initiating empirical treatment in critical scenarios, contributing to a positive patient outcome despite the diagnostic challenges.
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Affiliation(s)
- Miguel Costa
- Internal Medicine, Hospital Viana do Castelo, Viana do Castelo, PRT
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Wang X, Wei X, van der Zalm MM, Zhang Z, Subramanian N, Demers AM, Walters EG, Hesseling A, Liu C. Quantitation of Circulating Mycobacterium tuberculosis Antigens by Nanopore Biosensing in Children Evaluated for Pulmonary Tuberculosis in South Africa. ACS NANO 2023; 17:21093-21104. [PMID: 37643288 PMCID: PMC10668583 DOI: 10.1021/acsnano.3c04420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Nanopore sensing of proteomic biomarkers lacks accuracy due to the ultralow abundance of targets, a wide variety of interferents in clinical samples, and the mismatch between pore and analyte sizes. By converting antigens to DNA probes via click chemistry and quantifying their characteristic signals, we show a nanopore assay with several amplification mechanisms to achieve an attomolar level limit of detection that enables quantitation of the circulating Mycobacterium tuberculosis (Mtb) antigen ESAT-6/CFP-10 complex in human serum. The assay's nonsputum-based feature and low-volume sample requirements make it particularly well-suited for detecting pediatric tuberculosis (TB) disease, where establishing an accurate diagnosis is greatly complicated by the paucibacillary nature of respiratory secretions, nonspecific symptoms, and challenges with sample collection. In the clinical assessment, the assay was applied to analyze ESAT-6/CFP-10 levels in serum samples collected during baseline investigation for TB in 75 children, aged 0-12 years, enrolled in a diagnostic study conducted in Cape Town, South Africa. This nanopore assay showed superior sensitivity in children with confirmed TB (94.4%) compared to clinical "gold standard" diagnostic technologies (Xpert MTB/RIF 44.4% and Mtb culture 72.2%) and filled the diagnostic gap for children with unconfirmed TB, where these traditional technologies fell short. We envision that, in combination with automated sample processing and portable nanopore devices, this methodology will offer a powerful tool to support the diagnosis of pulmonary TB in children.
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Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina, 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Marieke M. van der Zalm
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Nandhini Subramanian
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Anne-Marie Demers
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa
- Division of Microbiology, Department of Laboratory Medicine, CHU Sainte-Justine, and Department of Microbiology, Immunology and Infectious Diseases, Faculty of Medicine, University of Montreal, Montreal, Quebec, H3T 1C5, Canada
| | - Elisabetta Ghimenton Walters
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Anneke Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina, 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina, 29208, USA
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Bhanushali J, Jadhav U, Ghewade B, Wagh P. Unveiling the Clinical Diversity in Nontuberculous Mycobacteria (NTM) Infections: A Comprehensive Review. Cureus 2023; 15:e48270. [PMID: 38054150 PMCID: PMC10695653 DOI: 10.7759/cureus.48270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023] Open
Abstract
Once considered rare, nontuberculous mycobacterial (NTM) infections have garnered increasing attention in recent years. This comprehensive review provides insights into the epidemiology, clinical diversity, diagnostic methods, treatment strategies, prevention, and emerging research trends in NTM infections. Key findings reveal the global prevalence of NTM infections, their diverse clinical presentations affecting respiratory and extra-pulmonary systems, and the diagnostic challenges addressed by advances in microbiological, radiological, and immunological methods. Treatment complexities, especially drug resistance and patient adherence, are discussed, along with the vulnerability of special populations. The importance of early detection and management is underscored. Prospects in NTM research, including genomics, diagnostics, drug development, and multidisciplinary approaches, promise to enhance our understanding and treatment of these infections. This review encapsulates the multifaceted nature of NTM infections, offering a valuable resource for clinicians, researchers, and public health professionals.
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Affiliation(s)
- Jay Bhanushali
- Respiratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Ulhas Jadhav
- Respiratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Babaji Ghewade
- Respiratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Pankaj Wagh
- Respiratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Aier S, Kalra S, Varma M, Pandey V. Atypical mycobacterium infection following anterior cruciate ligament reconstruction. BMJ Case Rep 2023; 16:e253440. [PMID: 37802587 PMCID: PMC10565175 DOI: 10.1136/bcr-2022-253440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
A man in his 20s presented with instability of the right knee following an incident of fall from a height. He was clinicoradiologically diagnosed to have an anterior cruciate ligament (ACL) tear for which he underwent ACL reconstruction. Postoperatively, he was started on an accelerated ACL rehabilitation protocol. Six weeks postoperatively, he developed features of subclinical septic arthritis for which he underwent arthroscopic debridement. Intraoperative samples cultured Mycobacterium abscessus complex on MGIT 960 system. The patient subsequently had to undergo another debridement after 1 month as there were clinical signs of persisting infection. The graft was intact even on the second debridement and after removing the implants. This case reports a rare complication of ACL reconstruction with infection by atypical mycobacterium and the clinical outcome. It also emphasises that prompt surgical intervention can save the graft.
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Affiliation(s)
- Sashitemjen Aier
- Orthopaedics, Kasturba Medical College Manipal, Manipal, Karnataka, India
| | - Saher Kalra
- Orthopaedics, Kasturba Medical College Manipal, Manipal, Karnataka, India
| | - Muralidhar Varma
- Infectious Diseases, Kasturba Medical College Manipal, Manipal, Karnataka, India
| | - Vivek Pandey
- Orthopaedics, Kasturba Medical College Manipal, Manipal, Karnataka, India
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Abbas AM, Bhandari J, Ngan A, Shahsavarani S, Verma RB. Lumbosacral Vertebral Osteomyelitis With Iliopsoas and Epidural Abscess Following Intravesical Bacillus Calmette-Guérin Therapy. Cureus 2023; 15:e47421. [PMID: 38021898 PMCID: PMC10658752 DOI: 10.7759/cureus.47421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
Intravesical Bacillus Calmette-Guérin (BCG) therapy is the gold-standard adjuvant therapy for patients with superficial or non-muscle-invasive bladder cancer. BCG is a live attenuated strain of Mycobacterium bovis, which induces an antitumor environment, effectively fighting malignant uroepithelial cells through cytotoxic reactions. However, BCG therapy may stimulate local or disseminated infections. In rare cases, vertebral osteomyelitis may arise in the thoracolumbar spine, mostly affecting older males. This is a case of an 84-year-old male patient who developed L5-S1 osteomyelitis with associated epidural and iliopsoas abscess. Symptoms manifested as severe low back pain and bilateral lower extremity weakness. This paper aims to raise awareness of and educate spine surgeons in recognizing this uncommon complication by taking into context a history of BCG therapy.
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Affiliation(s)
- Anas M Abbas
- Norton College of Medicine, Upstate University Hospital, Syracuse, USA
| | - Jenish Bhandari
- Internal Medicine, Upstate University Hospital, Syracuse, USA
| | - Alex Ngan
- Orthopedic Surgery, North Shore University Hospital-Long Island Jewish Medical Center, Manhasset, USA
| | - Shaya Shahsavarani
- Orthopedic Surgery, North Shore University Hospital-Long Island Jewish Medical Center, Manhasset, USA
| | - Rohit B Verma
- Orthopedic Surgery, North Shore University Hospital-Long Island Jewish Medical Center, Manhasset, USA
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Ouradou A, Veillette M, Bélanger Cayouette A, Corbin S, Boulanger C, Dorner S, Duchaine C, Bédard E. Effect of odor treatment systems on bioaerosol microbial concentration and diversity from wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162419. [PMID: 36858219 DOI: 10.1016/j.scitotenv.2023.162419] [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: 12/06/2022] [Revised: 01/30/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Biofiltration, activated carbon and chemical scrubbing are technologies used for odor control in wastewater treatment plants. These systems may also influence the airborne microbial load in treated air. The study objectives were to 1) evaluate the capacity of three odor control system technologies to reduce the airborne concentration of total bacteria, Legionella, L. pneumophila, non-tuberculous mycobacteria (NTM) and Cladosporium in winter and summer seasons and 2) to describe the microbial ecology of the biofiltration system and evaluate its impact on treated air microbial diversity. A reduction of the total bacterial concentration up to 25 times was observed after odor treatment. Quantification by qPCR revealed the presence of Legionella spp. in all air samples ranging between 26 and 1140 GC/m3, while L. pneumophila was not detected except for three samples below the limit of quantification. A significant increase of up to 25-fold of Legionella spp. was noticed at the outlet of two of the three treatment systems. NTM were ubiquitously detected before air treatment (up to 2500 GC/m3) and were significantly reduced by all 3 systems (up to 13-fold). Cladosporium was measured at low concentrations for each system (< 190 GC/m3), with 68 % of the air samples below the limit of detection. Biodiversity results revealed that biofiltration system is an active process that adapts to air pollutants over time. Legionella spp. were detected in significant abundance in the air once treated in winter (up to 27 %). Nevertheless, the abundance of protozoan hosts is low and does not explain the multiplication of Legionella spp. The season remains the most influential factor shaping biodiversity. In summer only, air biofiltration caused a significant enrichment of the biodiversity. Although odor control technologies are not designed for bacterial mitigation, findings from this study suggest their potential to reduce the abundance of some genera harboring pathogenic species.
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Affiliation(s)
- A Ouradou
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
| | - M Veillette
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada.
| | - A Bélanger Cayouette
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, University Laval, Québec, QC, Canada.
| | - S Corbin
- City of Repentigny, Repentigny, QC, Canada.
| | | | - S Dorner
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
| | - C Duchaine
- Research Center of the University Institute of Cardiology and Pneumology of Quebec-University Laval, Québec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, University Laval, Québec, QC, Canada; Canada Research Chair on Bioaerosols, University Laval, Québec, QC, Canada.
| | - E Bédard
- Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC, Canada.
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11
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Alonso-Moreno P, Rodriguez I, Izquierdo-Garcia JL. Benchtop NMR-Based Metabolomics: First Steps for Biomedical Application. Metabolites 2023; 13:metabo13050614. [PMID: 37233655 DOI: 10.3390/metabo13050614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics is a valuable tool for identifying biomarkers and understanding the underlying metabolic changes associated with various diseases. However, the translation of metabolomics analysis to clinical practice has been limited by the high cost and large size of traditional high-resolution NMR spectrometers. Benchtop NMR, a compact and low-cost alternative, offers the potential to overcome these limitations and facilitate the wider use of NMR-based metabolomics in clinical settings. This review summarizes the current state of benchtop NMR for clinical applications where benchtop NMR has demonstrated the ability to reproducibly detect changes in metabolite levels associated with diseases such as type 2 diabetes and tuberculosis. Benchtop NMR has been used to identify metabolic biomarkers in a range of biofluids, including urine, blood plasma and saliva. However, further research is needed to optimize the use of benchtop NMR for clinical applications and to identify additional biomarkers that can be used to monitor and manage a range of diseases. Overall, benchtop NMR has the potential to revolutionize the way metabolomics is used in clinical practice, providing a more accessible and cost-effective way to study metabolism and identify biomarkers for disease diagnosis, prognosis, and treatment.
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Affiliation(s)
- Pilar Alonso-Moreno
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ignacio Rodriguez
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jose Luis Izquierdo-Garcia
- NMR and Imaging in Biomedicine Group, Instituto Pluridisciplinar, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Chemistry in Pharmaceutical Sciences, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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12
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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Teo AKJ, Morishita F, Prem K, Eng S, An Y, Huot CY, Khun KE, Tieng S, Deng S, Tuot S, Yi S. Where are the missing people affected by tuberculosis? A programme review of patient-pathway and cascade of care to optimise tuberculosis case-finding, treatment and prevention in Cambodia. BMJ Glob Health 2023; 8:bmjgh-2022-010994. [PMID: 36921989 PMCID: PMC10030488 DOI: 10.1136/bmjgh-2022-010994] [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: 10/17/2022] [Accepted: 02/08/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND Cambodia has achieved great success in tuberculosis (TB) control in the past decade. Nevertheless, people with TB are missed by the health systems at different stages of the care pathway. This programme review corroborated the care-seeking behaviours of people with TB and TB services availability and estimated the number of people completing each step of the TB disease and TB preventive treatment (TPT) care cascade. METHODS Patient pathways and the care cascades for TB disease and TPT were constructed using data from the latest national TB prevalence survey, routine surveillance and programme, the global TB database and published studies. We also randomly selected TB survivors in the 2019 cohort to assess recurrence-free survival 1-year post-treatment. TPT care cascade was constructed for people living with HIV (PLHIV) and household contacts (children <5 years and all ages) of persons with bacteriologically-confirmed TB in 2019 and 2020. RESULTS Nationally, 54% of those who exhibited TB symptoms sought initial care in the private sector. Overall, 93% and 58% of people with presumptive TB did not access a facility with TB diagnostic and treatment services, respectively, at the first point of care-seeking. Approximately 56% (95% CI 52% to 57%) of the 47 000 (95% CI 31 000 to 68 000) estimated TB cases in 2019 achieved recurrence-free survival. Among the estimated PLHIV in Cambodia, <30% completed TPT. Among children <5 years, 53% (95% CI 29% to 65%) (2019) and 67% (95% CI 36% to 80%) (2020) of those eligible for TPT completed the regimen successfully. In 2019 and 2020, 23% (95% CI 22% to 25%) and 54% (95% CI 50% to 58%) of the estimated household contacts (all ages) eligible for TPT completed the regimen successfully. CONCLUSION There are significant gaps in care-seeking, coverage and access to TB services and TPT in Cambodia. Action plans to improve TB response have been co-developed with local stakeholders to address the gaps throughout the care cascades.
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Affiliation(s)
- Alvin Kuo Jing Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- The University of Sydney Institute for Infectious Diseases (Sydney ID) and the Centre of Research Excellence in Tuberculosis (TB-CRE), Sydney, NSW, Australia
| | - Fukushi Morishita
- World Health Organization Regional Office for the Western Pacific, Manila, Philippines
| | - Kiesha Prem
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sothearith Eng
- KHANA Center for Population Health Research, Phnom Penh, Cambodia
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yom An
- School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
- School of Public Health, National Institute of Public Health, Phnom Penh, Cambodia
- Sustaining Technical and Analytical Resources (STAR), Public Health Institute (PHI), Phnom Penh, Cambodia
| | - Chan Yuda Huot
- National Center for Tuberculosis and Leprosy Control (CENAT), Phnom Penh, Cambodia
| | - Kim Eam Khun
- National Center for Tuberculosis and Leprosy Control (CENAT), Phnom Penh, Cambodia
| | - Sivanna Tieng
- National Center for Tuberculosis and Leprosy Control (CENAT), Phnom Penh, Cambodia
| | - Serongkea Deng
- World Health Organization Cambodia Representative Office, Phnom Penh, Cambodia
| | - Sovannary Tuot
- KHANA Center for Population Health Research, Phnom Penh, Cambodia
- Faculty of Social Science and Humanities, Royal University of Phnom Penh, Phnom Penh, Cambodia
- Department of Community and Global Health, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Siyan Yi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- KHANA Center for Population Health Research, Phnom Penh, Cambodia
- Center for Global Health Research, Touro University California, Vallejo, California, USA
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Distinguishing nontuberculous mycobacterial lung disease and Mycobacterium tuberculosis lung disease on X-ray images using deep transfer learning. BMC Infect Dis 2023; 23:32. [PMID: 36658559 PMCID: PMC9854086 DOI: 10.1186/s12879-023-07996-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacterial lung disease (NTM-LD) and Mycobacterium tuberculosis lung disease (MTB-LD) have similar clinical characteristics. Therefore, NTM-LD is sometimes incorrectly diagnosed with MTB-LD and treated incorrectly. To solve these difficulties, we aimed to distinguish the two diseases in chest X-ray images using deep learning technology, which has been used in various fields recently. METHODS We retrospectively collected chest X-ray images from 3314 patients infected with Mycobacterium tuberculosis (MTB) or nontuberculosis mycobacterium (NTM). After selecting the data according to the diagnostic criteria, various experiments were conducted to create the optimal deep learning model. A performance comparison was performed with the radiologist. Additionally, the model performance was verified using newly collected MTB-LD and NTM-LD patient data. RESULTS Among the implemented deep learning models, the ensemble model combining EfficientNet B4 and ResNet 50 performed the best in the test data. Also, the ensemble model outperformed the radiologist on all evaluation metrics. In addition, the accuracy of the ensemble model was 0.85 for MTB-LD and 0.78 for NTM-LD on an additional validation dataset consisting of newly collected patients. CONCLUSIONS In previous studies, it was known that it was difficult to distinguish between MTB-LD and NTM-LD in chest X-ray images, but we have successfully distinguished the two diseases using deep learning methods. This study has the potential to aid clinical decisions if the two diseases need to be differentiated.
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Boldi MO, Denis-Lessard J, Neziri R, Brouillet R, von-Garnier C, Chavez V, Mazza-Stalder J, Jaton K, Greub G, Opota O. Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study. Front Cell Infect Microbiol 2023; 13:1131241. [PMID: 36936773 PMCID: PMC10017756 DOI: 10.3389/fcimb.2023.1131241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
Background The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests. Methods We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient. Results The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001). Conclusions PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.
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Affiliation(s)
- Marc-Olivier Boldi
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Justin Denis-Lessard
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Rina Neziri
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - René Brouillet
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Christophe von-Garnier
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Valérie Chavez
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Jesica Mazza-Stalder
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Katia Jaton
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
- *Correspondence: Onya Opota,
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Badr OI, Elrefaey WA, Shabrawishi M, Assaggaf HM, Minshawi F. Diagnostic accuracy of different bronchoscopic specimens in sputum Xpert MBT/RIF- negative pulmonary TB patients. Multidiscip Respir Med 2022; 17:872. [PMID: 36405489 PMCID: PMC9667574 DOI: 10.4081/mrm.2022.872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Background Tuberculosis (TB) control remains a critical public health problem worldwide. Rapid diagnosis and proper treatment are beneficial for the effective control of tuberculosis transmission. Diagnostic challenges arise when a patient has a clinical and radiological suspicion of tuberculosis but cannot produce sputum, sputum acid-fast bacilli, or Xpert Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) is negative, resulting in suboptimal management. As a result, more invasive techniques must be used on these patients to establish the diagnosis. Methods A retrospective study recruited 330 suspected pulmonary TB patients with negative sputum of Xpert MBT/RIF who underwent bronchoscopy between March 2018 and December 2021. The diagnostic yields of bronchoalveolar lavage fluid (acid-fast bacilli, Xpert MTB/RIF, and culture) and histopathologic examination (HPE) were calculated and compared to the final diagnosis and culture as a gold standard. Results Out of 330 suspected pulmonary TB patients, 181 had a final diagnosis of TB, and 149 had non-TB. The sensitivity of BALF (culture, Xpert, acid-fast bacilli) and trans-bronchial lung biopsy (HPE) was 80.7%, 72.9%, 21.1%, and 87.1%, respectively. Multiple nodules were associated with significantly higher BALF Xpert MTB, bronchoalveolar lavage fluid culture, and trans-bronchial lung biopsy (HPE) positivity. Conclusions Bronchoscopic specimens are essential for accurate and rapid diagnosis of sputum Xpert MBT/RIF negative patients with high clinical and radiological suspicion of tuberculosis.
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A New Artificial Intelligence-Based Method for Identifying Mycobacterium Tuberculosis in Ziehl–Neelsen Stain on Tissue. Diagnostics (Basel) 2022; 12:diagnostics12061484. [PMID: 35741294 PMCID: PMC9221616 DOI: 10.3390/diagnostics12061484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Mycobacteria identification is crucial to diagnose tuberculosis. Since the bacillus is very small, finding it in Ziehl–Neelsen (ZN)-stained slides is a long task requiring significant pathologist’s effort. We developed an automated (AI-based) method of identification of mycobacteria. We prepared a training dataset of over 260,000 positive and over 700,000,000 negative patches annotated on scans of 510 whole slide images (WSI) of ZN-stained slides (110 positive and 400 negative). Several image augmentation techniques coupled with different custom computer vision architectures were used. WSIs automatic analysis was followed by a report indicating areas more likely to present mycobacteria. Our model performs AI-based diagnosis (the final decision of the diagnosis of WSI belongs to the pathologist). The results were validated internally on a dataset of 286,000 patches and tested in pathology laboratory settings on 60 ZN slides (23 positive and 37 negative). We compared the pathologists’ results obtained by separately evaluating slides and WSIs with the results given by a pathologist aided by automatic analysis of WSIs. Our architecture showed 0.977 area under the receiver operating characteristic curve. The clinical test presented 98.33% accuracy, 95.65% sensitivity, and 100% specificity for the AI-assisted method, outperforming any other AI-based proposed methods for AFB detection.
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18
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Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective. Clin Microbiol Rev 2022; 35:e0017921. [PMID: 35612324 DOI: 10.1128/cmr.00179-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern medicine. Effective prevention strategies are urgently required to slow the emergence and further dissemination of AMR. Given the availability of data sets encompassing hundreds or thousands of pathogen genomes, machine learning (ML) is increasingly being used to predict resistance to different antibiotics in pathogens based on gene content and genome composition. A key objective of this work is to advocate for the incorporation of ML into front-line settings but also highlight the further refinements that are necessary to safely and confidently incorporate these methods. The question of what to predict is not trivial given the existence of different quantitative and qualitative laboratory measures of AMR. ML models typically treat genes as independent predictors, with no consideration of structural and functional linkages; they also may not be accurate when new mutational variants of known AMR genes emerge. Finally, to have the technology trusted by end users in public health settings, ML models need to be transparent and explainable to ensure that the basis for prediction is clear. We strongly advocate that the next set of AMR-ML studies should focus on the refinement of these limitations to be able to bridge the gap to diagnostic implementation.
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19
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Nonimaging Diagnostic Tests for Pneumonia. Radiol Clin North Am 2022; 60:521-534. [DOI: 10.1016/j.rcl.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Rinaldi I, Muthalib A, Gosal D, Wijayadi T, Sutedja B, Setiawan T, Gunawan A, Susanto N, Magdalena L, Handjari DR, Kurniawan F, Rifani A, Winston K. Abdominal Tuberculosis Mimicking Ovarian Cancer: A Case Report and Review of the Literature. Int Med Case Rep J 2022; 15:169-185. [PMID: 35431583 PMCID: PMC9012314 DOI: 10.2147/imcrj.s348434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Tuberculosis (TB) is a disease with high morbidity and mortality resulting from infection by Mycobacterium tuberculosis. TB can disseminate to any organ system of the body resulting in extrapulmonary tuberculosis. Interestingly, CA-125, which is a biomarker for some cancer, also rises in benign diseases such as pulmonary and extrapulmonary tuberculosis which may complicate diagnosis. In this case report, we present an abdominal tuberculosis patient that was initially presented as ovarian cancer. Case Report A 30-year-old woman admitted to the emergency department with chief complaint of fatigue and shortness of breath since 3 months ago. She had lost around 20 kg weight in the past 5 months. She was previously suspected with ovarian cancer because of the characteristic features of malignancy, high levels of CA-125, and positive PET scan. She was later diagnosed with abdominal TB. Subsequently, the patient was given anti-TB drugs, and the patient showed clinical improvement. Conclusion In the case of an elevated CA-125, clinicians should consider extrapulmonary TB as a differential diagnosis of ovarian cancer, especially in countries with high burden of tuberculosis.
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Affiliation(s)
- Ikhwan Rinaldi
- Divison of Hematology and Medical Oncology, Department of Internal Medicine, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Internal Medicine, Gading Pluit Hospital, Jakarta, Indonesia
- Correspondence: Ikhwan Rinaldi, Division of Hematology and Medical Oncology, Department of Internal Medicine, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia, Tel +62 811-177-997, Email
| | - Abdul Muthalib
- Divison of Hematology and Medical Oncology, Department of Internal Medicine, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Internal Medicine, Gading Pluit Hospital, Jakarta, Indonesia
| | - Djaja Gosal
- Department of Internal Medicine, Gading Pluit Hospital, Jakarta, Indonesia
| | - Teguh Wijayadi
- Department of Internal Medicine, Gading Pluit Hospital, Jakarta, Indonesia
| | - Barlian Sutedja
- Departement of General Surgery, Gading Pluit Hospital, Jakarta, Indonesia
| | - Tjondro Setiawan
- Departement of Radiology, Gading Pluit Hospital, Jakarta, Indonesia
| | - Andika Gunawan
- Departement of Nuclear Medicine, Gading Pluit Hospital, Jakarta, Indonesia
| | - Nelly Susanto
- Departement of Radiology, Gading Pluit Hospital, Jakarta, Indonesia
| | - Lingga Magdalena
- Departement of Radiology, Gading Pluit Hospital, Jakarta, Indonesia
| | - Diah Rini Handjari
- Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Departement of Pathology, Gading Pluit Hospital, Jakarta, Indonesia
| | - Fetisari Kurniawan
- Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Departement of Pathology, Gading Pluit Hospital, Jakarta, Indonesia
| | - Aisyah Rifani
- Departement of Internal Medicine, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Kevin Winston
- Departement of Internal Medicine, Cipto Mangunkusumo National General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Culture-proven disseminated Mycobacterium Bovis infection (BCG-Osis) following intravesical BCG immunotherapy in a patient with bladder carcinoma-in-situ: ‘Case report’. AFRICAN JOURNAL OF UROLOGY 2022. [DOI: 10.1186/s12301-022-00270-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWe are reporting a case of culture-proven disseminated Mycobacterium Bovis infection (BCG-Osis), involving lung, bone-marrow and urinary tract, after intravesical Bacillus Calmette–Guérin (BCG) immunotherapy for bladder carcinoma-in-situ. A 71-year-gentleman presented with fever shortly after intravesical BCG instillation. He was initially treated for presumed Urinary Tract Infection, but negative urine culture and persistent fever prompted us to consider alternative diagnoses. Empirical treatment for BCG-Osis was commenced after initial negative workup including blood culture, echocardiography, computed tomography (CT) Chest, and Kidney-Ureter-Bladder (KUB). However, he remained febrile and leukopenic, so bone-marrow examination was performed along with repeating CT Chest, which revealed non-caseating granulomas and small nonspecific pulmonary nodules, respectively, supporting our provisional diagnosis. Interestingly, Mycobacterium Bovis was finally isolated from one of his urine specimens, confirming our diagnosis.
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22
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Soetaert K, Ceyssens PJ, Boarbi S, Bogaerts B, Delcourt T, Vanneste K, De Keersmaecker SC, Roosens NH, Vodolazkaia A, Mukovnikova M, Mathys V. Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019. Acta Clin Belg 2021; 77:853-860. [PMID: 34751641 DOI: 10.1080/17843286.2021.1999588] [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] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Since January 2019, the Belgian National Reference Center for Mycobacteria (NRC) has switched from conventional typing to prospective whole-genome sequencing (WGS) of all submitted Mycobacterium tuberculosis complex (MTB) isolates. The ISO17025 validated procedure starts with semi-automated extraction and purification of gDNA directly from the submitted MGIT tubes, without preceding subculturing. All samples are then sequenced on an Illumina MiSeq sequencer and analyzed using an in-house developed and validated bioinformatics workflow to determine the species and antimicrobial resistance. In this study, we retrospectively compare results obtained via WGS to conventional phenotypic and genotypic testing, for all Belgian MTB strains analyzed in 2019 (n = 306). RESULTS In all cases, the WGS-based procedure was able to identify correctly the MTB species. Compared to MGIT drug susceptibility testing (DST), the sensitivity and specificity of genetic prediction of resistance to first-line antibiotics were respectively 100 and 99% (rifampicin, RIF), 90.5 and 100% (isoniazid, INH), 100 and 98% (ethambutol, EMB) and 61.1 and 100% (pyrazinamide, PZA). The negative predictive value was above 95% for these four first-line drugs. A positive predictive value of 100% was calculated for INH and PZA, 80% for RIF and 45% for EMB. CONCLUSIONS Our study confirms the effectiveness of WGS for the rapid detection of M. tuberculosis complex and its drug resistance profiles for first-line drugs even when working directly on MGIT tubes, and supports the introduction of this test into the routine workflow of laboratories performing tuberculosis diagnosis.
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Affiliation(s)
- Karine Soetaert
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Pieter-Jan Ceyssens
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Samira Boarbi
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels, Belgium
| | | | - Nancy H.C. Roosens
- Transversal Activities in Applied Genomics (TAG), Sciensano, Brussels, Belgium
| | | | | | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
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Catalytic ferromagnetic gold nanoparticle immunoassay for the detection and differentiation of Mycobacterium tuberculosis and Mycobacterium bovis. Anal Chim Acta 2021; 1184:339037. [PMID: 34625241 DOI: 10.1016/j.aca.2021.339037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022]
Abstract
A ferromagnetic gold nanoparticle based immune detection assay, exploiting the enhanced signal amplification of inorganic nanozymes, was developed and evaluated for its potential application in the detection of Mycobacterium tuberculosis complex (MTBC) organisms, and simultaneous identification of Mycobacterium bovis. Ferromagnetic gold nanoparticles (Au-Fe3O4 NPs) were prepared and their intrinsic peroxidase-like activity exploited to catalyse 3,3',5',5-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2). When the Au-Fe3O4 NPs were functionalised by direct coupling with MTBC-selective antibodies, a nanoparticle based immune detection assay (NPIDA) was developed which could detect Mycobacterium tuberculosis (MTB) and differentiate M. bovis. In the assay, the intrinsic magnetic capability of the functionalised Au-Fe3O4 NPs was used in sample preparation to capture target bacterial cells. These were incorporated into a novel immunoassay which used species selective monoclonal antibodies (mAb) to detect bound target. The formation of a blue TMB oxidation product, with a peak absorbance of 370 nm, indicated successful capture and identification of the target. The detection limit of the NPIDA for both MTB and M. bovis was determined to be comparable to conventional ELISA using the same antibodies. Although limited matrix effects were observed in either assay, the NPIDA offers a reduced time to confirmatory identification. This novel NPIDA was capable of simultaneous sample concentration, purification, immunological detection and speciation. To our knowledge, it represents the first immune-based diagnostic test capable of identifying MTBC organisms and simultaneously differentiating M. bovis.
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Vongthilath-Moeung R, Poncet A, Renzi G, Schrenzel J, Janssens JP. Time to Detection of Growth for Mycobacterium tuberculosis in a Low Incidence Area. Front Cell Infect Microbiol 2021; 11:704169. [PMID: 34490143 PMCID: PMC8418320 DOI: 10.3389/fcimb.2021.704169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/04/2021] [Indexed: 01/29/2023] Open
Abstract
Background Diagnosis of Mycobacterium tuberculosis (MTB) infection can be confirmed by Xpert assays within hours. However, when sample size does not allow performing both culture and Xpert, or if Xpert is negative, then formal diagnosis of MTB relies on culture and time to detection of growth (TDG) becomes critical for clinical management. Objectives To determine TDG in Xpert negative samples, or in samples in which Xpert could not be performed, in a low-incidence area for MTB. Methods Retrospective analysis (2015-2020) of a database including all cultures for mycobacteria in a University Hospital covering approximately 500'000 inhabitants. Analysis was restricted to culture positive (C+) samples for MTB for which 1/Xpert was negative or could not be performed because of limited sample volume, and 2/collected from subjects treated less than 24 hours. TDG was analyzed according to microscopy, origin of sample (pulmonary or not) and presence of cavitation. Results Among 837 C+ samples for MTB, 236 samples (80% of respiratory origin) from 147 patients fulfilled study criteria; 78 samples (49 patients, 33%) were acid-fast bacilli (AFB) positive. Median (IQR) TDG was 25 (17; 40) days for all samples. TDG exceeded 28 days in 43% of samples and was significantly shorter in AFB+ vs AFB- samples, and samples from cavitary vs non cavitary or extra-thoracic disease. Conclusions In Xpert negative samples, or samples for which Xpert could not be performed, TDG exceeded 4 weeks in 43% of samples. AFB+ and samples from cavitary lung disease had a significantly shorter TDG.
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Affiliation(s)
| | - Antoine Poncet
- Center for Clinical Research & Division of Clinical-Epidemiology, Department of Health and Community Medicine, University of Geneva, University Hospitals of Geneva, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Jean-Paul Janssens
- Division of Pulmonary Diseases, Geneva University Hospitals, Geneva, Switzerland
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Value of Xpert MTB/RIF Using Bronchoalveolar Lavage Fluid for the Diagnosis of Pulmonary Tuberculosis: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:JCM.02170-20. [PMID: 33177121 DOI: 10.1128/jcm.02170-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The performance of Xpert MTB/RIF using bronchoalveolar lavage fluid (BAL) for the diagnosis of pulmonary tuberculosis (PTB) remains unclear. Therefore, a systematic review/meta-analysis was conducted. Studies published before 31 December 2019 were retrieved from the PubMed, Embase, and Web of Science databases using the keywords "pulmonary tuberculosis," "Xpert MTB/RIF," and "BAL." Two independent evaluators extracted the data and assessed the bias risk of the included studies. A random-effects model was used to calculate the overall sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR, respectively), diagnostic odds ratio (DOR), and the area under the curve (AUC), as well as the respective 95% confidence intervals (CIs). Nineteen trials involving 3,019 participants met the inclusion criteria. Compared to the culture method, the pooled sensitivity, specificity, PLR, NLR, DOR, and the AUC with 95% CIs of Xpert MTB/RIF were 0.87 (0.84 to 0.90), 0.92 (0.91 to 0.93), 10.21 (5.78 to 18.02), 0.16 (0.12 to 0.22), 78.95 (38.59 to 161.53), and 0.9467 (0.9462 to 0.9472), respectively. Relative to the composite reference standard, the observed values were 0.69 (0.65 to 0.72), 0.98 (0.98 to 0.99), 37.50 (18.59 to 75.62), 0.30 (0.21 to 0.43), 171.98 (80.82 to 365.96), and 0.9691 (0.9683 to 0.9699), respectively. All subgroups, except children, showed high sensitivity and specificity. In conclusion, the use of Xpert MTB/RIF in the context of BAL samples has a high diagnostic performance for PTB (except for children) and may serve as an alternative rapid diagnostic tool.
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Guan Y, Zeng Z. Elbow arthroplasty complicated by Mycobacterium tuberculosis infection: A case report. Medicine (Baltimore) 2021; 100:e24376. [PMID: 33655913 PMCID: PMC7939209 DOI: 10.1097/md.0000000000024376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Total elbow arthroplasty (TEA) is an orthopedic procedure that is relatively infrequently performed, but its use has been increasing over time. Infection remains one of the most concerning complications after TEA, although Mycobacterium tuberculosis (TB) as a microbial etiology, is extremely rare. Here, we present a case of M. tuberculosis infection after TEA. PATIENT CONCERNS A 45-year-old woman underwent TEA for severe traumatic arthritis of the elbow following failure of conservative treatment. Four months after TEA, the patient experienced progressive elbow pain and swelling, without other external signs of infection such as a sensation of local heating and erythematous alterations. DIAGNOSIS Pulmonary computed tomography showed stable pulmonary TB in the right upper lobe. The T-SPOT, TB, and purified protein derivative test results were positive, and M. tuberculosis exhibited growth on cultures. The final diagnosis was periprosthetic infection of M. tuberculosis. INTERVENTIONS The patient was treated with debridement with submission of deep tissue cultures. According to these cultures and suggestions of a bacteriologist, anti-TB treatment was administered for 12 months. OUTCOMES The symptoms of the infection were controlled, and the prosthesis was retained. At the time of writing this case report, the elbow prosthesis had survived for more than 2 years, and no recurrent infection had been observed. CONCLUSION The diagnosis of TB infection after TEA is difficult to confirm due to its nonspecific signs and symptoms. Despite the extremely low incidence, failure to consider this possibility for diagnosis can lead to delayed treatment. Proper diagnosis allows for antitubercular therapy with retention of a prosthesis.
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Affiliation(s)
| | - Zhimin Zeng
- Department of Orthopaedic Surgery, Ningbo No. 6 Hospital, Ningbo, Zhejiang, China
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Bae JY, Yun IS, Roh TS, Kim YS. Treatment strategy for skin and soft tissue infections caused by nontuberculous mycobacteria following various procedures. ARCHIVES OF AESTHETIC PLASTIC SURGERY 2021. [DOI: 10.14730/aaps.2020.02327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Izquierdo-Garcia JL, Comella-Del-Barrio P, Campos-Olivas R, Villar-Hernández R, Prat-Aymerich C, De Souza-Galvão ML, Jiménez-Fuentes MA, Ruiz-Manzano J, Stojanovic Z, González A, Serra-Vidal M, García-García E, Muriel-Moreno B, Millet JP, Molina-Pinargote I, Casas X, Santiago J, Sabriá F, Martos C, Herzmann C, Ruiz-Cabello J, Domínguez J. Discovery and validation of an NMR-based metabolomic profile in urine as TB biomarker. Sci Rep 2020; 10:22317. [PMID: 33339845 PMCID: PMC7749110 DOI: 10.1038/s41598-020-78999-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Despite efforts to improve tuberculosis (TB) detection, limitations in access, quality and timeliness of diagnostic services in low- and middle-income countries are challenging for current TB diagnostics. This study aimed to identify and characterise a metabolic profile of TB in urine by high-field nuclear magnetic resonance (NMR) spectrometry and assess whether the TB metabolic profile is also detected by a low-field benchtop NMR spectrometer. We included 189 patients with tuberculosis, 42 patients with pneumococcal pneumonia, 61 individuals infected with latent tuberculosis and 40 uninfected individuals. We acquired the urine spectra from high and low-field NMR. We characterised a TB metabolic fingerprint from the Principal Component Analysis. We developed a classification model from the Partial Least Squares-Discriminant Analysis and evaluated its performance. We identified a metabolic fingerprint of 31 chemical shift regions assigned to eight metabolites (aminoadipic acid, citrate, creatine, creatinine, glucose, mannitol, phenylalanine, and hippurate). The model developed using low-field NMR urine spectra correctly classified 87.32%, 85.21% and 100% of the TB patients compared to pneumococcal pneumonia patients, LTBI and uninfected individuals, respectively. The model validation correctly classified 84.10% of the TB patients. We have identified and characterised a metabolic profile of TB in urine from a high-field NMR spectrometer and have also detected it using a low-field benchtop NMR spectrometer. The models developed from the metabolic profile of TB identified by both NMR technologies were able to discriminate TB patients from the rest of the study groups and the results were not influenced by anti-TB treatment or TB location. This provides a new approach in the search for possible biomarkers for the diagnosis of TB.
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Affiliation(s)
- José Luis Izquierdo-Garcia
- CIC biomaGUNE Center for Cooperative Research in Biomaterials, BRTA Basque Research and Technology Alliance, Donostia, Donostia, Gipuzkoa, Spain
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Patricia Comella-Del-Barrio
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Raquel Villar-Hernández
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Prat-Aymerich
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Maria Luiza De Souza-Galvão
- Unitat de Tuberculosi de Drassanes, Servei de Pneumologia, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Juan Ruiz-Manzano
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Zoran Stojanovic
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Adela González
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Mar Serra-Vidal
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Esther García-García
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Beatriz Muriel-Moreno
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Joan Pau Millet
- Serveis Clínics, Unitat Clínica de Tractament Directament Observat de la Tuberculosi, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Israel Molina-Pinargote
- Serveis Clínics, Unitat Clínica de Tractament Directament Observat de la Tuberculosi, Barcelona, Spain
| | - Xavier Casas
- Serveis Clínics, Unitat Clínica de Tractament Directament Observat de la Tuberculosi, Barcelona, Spain
| | - Javier Santiago
- Serveis Clínics, Unitat Clínica de Tractament Directament Observat de la Tuberculosi, Barcelona, Spain
| | - Fina Sabriá
- Servei de Pneumologia, Hospital Sant Joan Despí Moises Broggi, Sant Joan Despi, Barcelona, Spain
| | - Carmen Martos
- Servei de Pneumologia, Hospital Sant Joan Despí Moises Broggi, Sant Joan Despi, Barcelona, Spain
| | | | - Jesús Ruiz-Cabello
- CIC biomaGUNE Center for Cooperative Research in Biomaterials, BRTA Basque Research and Technology Alliance, Donostia, Donostia, Gipuzkoa, Spain
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Vizcaya, Spain
| | - José Domínguez
- CIBER de enfermedades respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, Spain.
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Lee JY, Kim BJ, Kim JM, Kim J, Joh JS, Jeong I, Kook YH, Kim BJ. Usefulness of the IgA and IgG Responses to Macrophage Migration Inhibitory Factor for the Diagnosis of Tuberculosis. Diagnostics (Basel) 2020; 10:diagnostics10110991. [PMID: 33238656 PMCID: PMC7700399 DOI: 10.3390/diagnostics10110991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/21/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
Serological tests offer the potential in order to improve the diagnosis of tuberculosis (TB). Macrophage migration inhibitory factor (MIF) plays a protective role in infection control in TB; however, to date, no studies on antibody responses to MIF have been reported. We measured immunoglobulin (Ig)A and IgG responses to MIF in individuals with either active tuberculosis (ATB; n = 65), latent tuberculosis (LTBI; n = 53), or in non-infected individuals (NI; n = 62). The QuantiFERON-TB Gold In-Tube (QFT-GIT) assay was used in order to screen for LTBI. The level of IgA against MIF was significantly lower in LTBI and ATB patients than in NI individuals, was significantly related to LTBI and ATB diagnosis, and it could discriminate between LTBI and ATB. In contrast, the level of IgG against MIF was significantly lower in LTBI patients than in NI individuals and was significantly related to LTBI diagnosis. Anti-MIF IgG levels were significantly lower in AFB-negative TB, minimal TB, and new ATB patients, than in the NI group. IgA and IgG levels against MIF both showed significant negative correlations with IFN-γ levels, as assessed using the QFT-GIT test. Although none of the antibodies could achieve high diagnostic predictive power individually, our results suggest the possibility of using IgA antibody responses to MIF in the diagnosis of LTBI and ATB.
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Affiliation(s)
- Ji Yeon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Korea; (J.Y.L.); (J.K.); (J.K.); (J.-S.J.); (I.J.)
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Jee-min Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Korea; (J.Y.L.); (J.K.); (J.K.); (J.-S.J.); (I.J.)
| | - Junghyun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Korea; (J.Y.L.); (J.K.); (J.K.); (J.-S.J.); (I.J.)
| | - Joon-Sung Joh
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Korea; (J.Y.L.); (J.K.); (J.K.); (J.-S.J.); (I.J.)
| | - Ina Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Korea; (J.Y.L.); (J.K.); (J.K.); (J.-S.J.); (I.J.)
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea;
- Correspondence: (Y.-H.K.); (B.-J.K.); Tel.: +82-2-740-8306 (Y.-H.K.); +82-2-740-8316 (B.-J.K.)
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea;
- Correspondence: (Y.-H.K.); (B.-J.K.); Tel.: +82-2-740-8306 (Y.-H.K.); +82-2-740-8316 (B.-J.K.)
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Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis 2020; 96:48-53. [DOI: 10.1016/j.ijid.2020.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/19/2022] Open
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Detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP. Sci Rep 2020; 10:7874. [PMID: 32398743 PMCID: PMC7217866 DOI: 10.1038/s41598-020-64708-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/15/2020] [Indexed: 12/30/2022] Open
Abstract
Accurate drug resistance detection is key for guiding effective tuberculosis treatment. While genotypic resistance can be rapidly detected by molecular methods, their application is challenged by mixed mycobacterial populations comprising both susceptible and resistant cells (heteroresistance). For this, next-generation sequencing (NGS) based approaches promise the determination of variants even at low frequencies. However, accurate methods for a valid detection of low-frequency variants in NGS data are currently lacking. To tackle this problem, we developed the variant detection tool binoSNP which allows the determination of low-frequency single nucleotide polymorphisms (SNPs) in NGS datasets from Mycobacterium tuberculosis complex (MTBC) strains. By taking a reference-mapped file as input, binoSNP evaluates each genomic position of interest using a binomial test procedure. binoSNP was validated using in-silico, in-vitro, and serial patient isolates datasets comprising varying genomic coverage depths (100-500×) and SNP allele frequencies (1-30%). Overall, the detection limit for low-frequency SNPs depends on the combination of coverage depth and allele frequency of the resistance-associated mutation. binoSNP allows for valid detection of resistance associated SNPs at a 1% frequency with a coverage ≥400×. In conclusion, binoSNP provides a valid approach to detect low-frequency resistance-mediating SNPs in NGS data from clinical MTBC strains. It can be implemented in automated, end-user friendly analysis tools for NGS data and is a step forward towards individualized TB therapy.
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Meegada S, Gyamfi R, Muppidi V, Dandu V, Challa T. Multiple Intracranial Tuberculomas with an Intra-medullary Spinal Cord Tuberculoma in a Pediatric Patient. Cureus 2020; 12:e7248. [PMID: 32292663 PMCID: PMC7152571 DOI: 10.7759/cureus.7248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 11/10/2022] Open
Abstract
Central nervous system (CNS) tuberculosis (TB), caused by Mycobacterium tuberculosis (MT), is a severe form of TB, which presents as meningitis, cerebritis, abscesses, spinal tuberculous arachnoiditis, and rarely tuberculomas. CNS TB is prevalent in the underdeveloped or developing world and is common in malnourished, alcoholics, children, young adults, immunocompromised, and cancer patients. Intracranial tuberculomas (ICT) can present with symptoms and signs of focal neurological deficits with or without systemic manifestations. ICT is the least common presentation of CNS TB. Medical management with anti-TB drugs and steroids is the mainstay of treatment, while surgical intervention is usually reserved for refractory cases. Here, we present the case of a 10-year-old Indian American girl with headaches, diplopia, fever, and neck pain diagnosed with ICT and intramedullary spinal cord tuberculoma.
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Affiliation(s)
- Sreenath Meegada
- Internal Medicine, The University of Texas Health Science Center/Christus Good Shepherd Medical Center, Longview, USA
| | | | | | - Vasuki Dandu
- Neurology, Baptist Health Medical Center, Little Rock, USA
| | - Tejo Challa
- Internal Medicine, The University of Texas Health Science Center/Christus Good Shepherd Medical Center, Longview, USA
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Trautman C, Da Costa JR, Cortese C, Aslam N. Prosthetic valve endocarditis from Mycobacterium chimaera infection causing granulomatous interstitial nephritis. IDCases 2020; 20:e00733. [PMID: 32154105 PMCID: PMC7057185 DOI: 10.1016/j.idcr.2020.e00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium chimaera is a rare infection associated with cardiopulmonary bypass. We describe a case of granulomatous interstitial nephritis caused by M. chimaera in a patient with prosthetic aortic valve endocarditis. A 63-year-old female with a mechanical aortic valve replacement developed fatigue, 20 lbs. weight loss, anemia, and an elevated creatinine. Fat pad aspirate at an outside hospital was suspicious for amyloidosis which prompted hematology referral at our institution. Bone marrow biopsy revealed a single granuloma, negative for amyloid or acid fast bacillus (AFB). She was admitted to our hospital for worsening kidney function refractory to intravenous fluid challenge. Transesophageal echocardiogram showed aortic root abscess and valve vegetation with negative blood cultures at seven days. Renal biopsy showed granulomatous interstitial nephritis and negative AFB stain. Prednisone 40 mg was started and renal function partially improved. Blood cultures obtained before biopsy subsequently grew M. chimaera. Three-drug antimicrobial therapy was initiated and prednisone discontinued. One month later, creatinine improved and follow up echocardiogram showed no lesion. Our case highlights this rare infection inducing granulomatous interstitial nephritis despite lack of positive AFB or gram stains on renal biopsy.
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Affiliation(s)
- Christopher Trautman
- Department of Medicine, Division of Nephrology & Hypertension, Mayo Clinic, FL, United States
| | - Jonathan R Da Costa
- Department of Medicine, Division of Nephrology & Hypertension, Mayo Clinic, FL, United States
| | | | - Nabeel Aslam
- Department of Medicine, Division of Nephrology & Hypertension, Mayo Clinic, FL, United States
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Shi SD, Hsueh PR, Yang PC, Chou CC. Use of DosR Dormancy Antigens from Mycobacterium tuberculosis for Serodiagnosis of Active and Latent Tuberculosis. ACS Infect Dis 2020; 6:272-280. [PMID: 31815418 DOI: 10.1021/acsinfecdis.9b00329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As more than two billion people possibly have a latent tuberculosis (LTB) infection, early LTB diagnosis is crucial for the efficient control and elimination of tuberculosis (TB). The aim of this study is to detect the serum antibody responses to dormancy-related DosR regulon antigens of Mycobacterium tuberculosis for the diagnosis of active and latent TB infections. A membrane array with 25 latency antigens detected by silver-enhanced gold nanoparticles was used to determine the corresponding cognate antibody levels in clinical serum samples from healthy controls, TB patients, and individuals with LTB. The array is sized to fit into a 24-well ELISA plate and follows an ELISA-like experimental procedure without expensive instrumentation. Linear discriminant analysis (LDA) of the resulting antibody profiling data set identified a panel of nine DosR antigens with significant discriminatory capability among different subjects with ≥90% sensitivity, specificity, and overall accuracy. Furthermore, the high predictive performance validated by an independent test sample set reflects the robustness and reliability of the LDA classification model. Our current data demonstrate that the nine DosR antigen combination associated with the proposed membrane array platform is a clinically feasible approach for distinguishing different TB infection statuses. The proposed methodology in this study could be further developed for multiple disease serodiagnoses with high sensitivity and specificity.
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Affiliation(s)
- Sheng-Dong Shi
- Department of Biomedical Sciences and Institute of Molecular Biology, National Chung Cheng University, No. 168 University Road, Min-Hsiung, Chia-Yi, Taiwan 62102, ROC
- Division of Laboratory Medicine, Chia-Yi and Wanqiao Branch, Taichung Veterans General Hospital, No. 600 Shixian Rd., Chia-Yi City, Taiwan 60090, ROC
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University College of Medicine, No. 1 Jen Ai Road, Taipei, Taiwan 10051, ROC
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University College of Medicine, No. 1 Jen Ai Road, Taipei, Taiwan 10051, ROC
| | - Cheng-Chung Chou
- Department of Biomedical Sciences and Institute of Molecular Biology, National Chung Cheng University, No. 168 University Road, Min-Hsiung, Chia-Yi, Taiwan 62102, ROC
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Colucciello M. Mycobacterium chimaera chorioretinitis as a biomarker of systemic disease activity following nosocomial acquisition during cardiopulmonary bypass. Postgrad Med 2019; 132:167-171. [PMID: 31766930 DOI: 10.1080/00325481.2019.1697545] [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] [Indexed: 10/25/2022]
Abstract
Objectives: To understand the role of ophthalmoscopic examination (dilated retina examination and widefield fundus photography) in the diagnosis and management of nosocomial acquisition of Mycobacterium chimaera following open heart surgery with cardiopulmonary bypass utilizing a heater-cooler unit, an entity that is associated with >50% mortality during the worldwide outbreak that has occurred since 2013.Methods: Case report with review of previous cases.Results: Signature Mycobacterium chimaera chorioretinal lesions can be used as a diagnostic sign and a biomarker for assessment of treatment efficacy.Conclusions: Ophthalmologic examination can play a key role in diagnosis and management of systemic Mycobacterium chimaera following cardiopulmonary bypass; such examinations may yield earlier diagnosis, diminishing mortality rates.
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Affiliation(s)
- Michael Colucciello
- Clinical Associate, University of Pennsylvania School of Medicine; Retina Specialist, Vantage Eye Care, South Jersey Eye Physicians Division, Moorestown, NJ, USA
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Rathish B, Wilson A, Pillay R, Warrier A, Philips G. A Bundled Approach to Pulmonary Tuberculosis Testing: Experience from a Tertiary Care Centre in South India. Cureus 2019; 11:e6042. [PMID: 31824808 PMCID: PMC6886623 DOI: 10.7759/cureus.6042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The diagnosis of pulmonary tuberculosis (PTB) is based on a stepwise approach consisting of sputum microscopy and molecular testing (GeneXpert), with the use of Mycobacterium culture in select cases. We analysed a bundled approach of PTB testing, consisting of all three of these tests during the patient's first visit, for all patients fitting into the clinical criteria of PTB. We retrospectively analysed the medical records of all patients who underwent the TB diagnosis bundle during a period of 29 months. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of sputum microscopy and GeneXpert were compared against the gold standard of Mycobacterium culture. The incremental yield of diagnosing PTB by addition of Mycobacterium culture in the diagnostic bundle during the initial testing was also calculated. The bundled approach conferred an advantage in terms of faster clinical decision and increased diagnosis rates, by virtue of the speed of smear microscopy and GeneXpert, combined with the higher sensitivity of culture. The bundle also had the additional benefit of detecting non-tuberculous Mycobacterium (NTM) by the culture method. Hence we feel that the bundled approach ensures fewer number of hospital visits and reduces the potential delays in a clinical decision making.
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Affiliation(s)
| | - Arun Wilson
- Infectious Diseases, Aster Medcity, Kochi, IND
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Tu Phan LM, Tufa LT, Kim HJ, Lee J, Park TJ. Trends in Diagnosis for Active Tuberculosis Using Nanomaterials. Curr Med Chem 2019; 26:1946-1959. [DOI: 10.2174/0929867325666180912105617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022]
Abstract
Background:Tuberculosis (TB), one of the leading causes of death worldwide, is difficult to diagnose based only on signs and symptoms. Methods for TB detection are continuously being researched to design novel effective clinical tools for the diagnosis of TB.Objective:This article reviews the methods to diagnose TB at the latent and active stages and to recognize prospective TB diagnostic methods based on nanomaterials.Methods:The current methods for TB diagnosis were reviewed by evaluating their advantages and disadvantages. Furthermore, the trends in TB detection using nanomaterials were discussed regarding their performance capacity for clinical diagnostic applications.Results:Current methods such as microscopy, culture, and tuberculin skin test are still being employed to diagnose TB, however, a highly sensitive point of care tool without false results is still needed. The utilization of nanomaterials to detect the specific TB biomarkers with high sensitivity and specificity can provide a possible strategy to rapidly diagnose TB. Although it is challenging for nanodiagnostic platforms to be assessed in clinical trials, active TB diagnosis using nanomaterials is highly expected to achieve clinical significance for regular application. In addition, aspects and future directions in developing the high-efficiency tools to diagnose active TB using advanced nanomaterials are expounded.Conclusion:This review suggests that nanomaterials have high potential as rapid, costeffective tools to enhance the diagnostic sensitivity and specificity for the accurate diagnosis, treatment, and prevention of TB. Hence, portable nanobiosensors can be alternative effective tests to be exploited globally after clinical trial execution.
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Affiliation(s)
- Le Minh Tu Phan
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Halal Industrialization Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea
| | - Lemma Teshome Tufa
- Department of Nano Fusion and Cogno-Mechatronics Engineering, Pusan National University, 2 Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Hwa-Jung Kim
- Department of Microbiology and Research Institute for Medical Science, College of Medicine, Chungnam National University, 266 Munhwa- ro, Jung-gu, Daejeon 35015, Korea
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Jung Park
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Halal Industrialization Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea
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Whole-Genome Sequencing in Relation to Resistance of Mycobacterium Tuberculosis. ACTA MEDICA MARTINIANA 2019. [DOI: 10.2478/acm-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract
Tuberculosis, a disease caused by Mycobacterium tuberculosis, represents one of the deadliest infections worldwide. The incidence of resistant forms is increasing year by year; therefore, it is necessary to involve new methods for rapid diagnostics and treatment. One of the possible solutions is the use of whole-genome sequencing (WGS).
The WGS provides an identification of complete genome of the microorganism, including all genes responsible for resistance, in comparison with other genotypic methods (eg. Xpert MTB / RIF or Hain line-probes) that are capable to detect only basic genes. WGS data are available in 1-9 days and several online software tools (TBProfiler, CASTB, Mykrobe PredictorTB) are used for their interpretation and analysis, compared to 3-8 weeks in the case of classic phenotypic evaluation.
Furthermore, WGS predicts resistance to the first-line antituberculotics with a sensitivity of 85-100% and a specificity of 85-100%.
This review elucidates the importance and summarizes the current knowledge about the possible use of WGS in diagnosis and treatment of resistant forms of tuberculosis elucidates.
WGS of M. tuberculosis brings new possibilities for rapid and accurate diagnostics of resistant forms of tuberculosis. Introducing WGS into routine practice can help to reduce the spread of resistant forms of tuberculosis as well as to increase the success rate of the treatment, especially through an appropriate combination of antituberculotics ATs. Introduction of WGS into routine diagnostics can, in spite of the financial difficulty, significantly improve patient care.
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Bi AS, Li D, Ma Y, Wu D, Ma Y. Mycobacterium tuberculosis as a Cause of Periprosthetic Joint Infection After Total Knee Arthroplasty: A Review of the Literature. Cureus 2019; 11:e4325. [PMID: 31183304 PMCID: PMC6538407 DOI: 10.7759/cureus.4325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/26/2019] [Indexed: 01/21/2023] Open
Abstract
Total knee arthroplasty (TKA) has become one of the most popular and successful surgeries performed in the world. Infection remains one of the most dreaded complications following TKA, and while rare, tuberculosis as a microbial etiology remains difficult to both diagnose and treat. A review was performed using PubMed, the Cochrane Database of Systematic Reviews, and EMBASE to identify literature pertinent to Mycobacterium tuberculosis infection, TKAs, periprosthetic joint infections, and any combination of the three. The diagnosis of tuberculosis infection after TKA is difficult due to nonspecific signs and symptoms and diagnostic testing. The surgeon should use a comprehensive approach to incorporate the patient's medical history, physical exam, and blood and imaging diagnostics. Among these, bacterial culture and histopathological examination remain the gold standard of diagnosis, but Polymerase chain reaction technology offers another, more sensitive and rapid option. Treatment strategy centers around on the cornerstone of anti-tuberculosis medical therapy and surgery depending on the clinical situation. While there is a lack of primary literature and standardized guidelines for the diagnosis and treatment of tuberculosis infection after TKA, the overarching principles of the treatment of tuberculosis and the treatment of the periprosthetic infection can be implemented together. There remains room for original research and improvements in both diagnostic testing and treatment.
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Affiliation(s)
- Andrew S Bi
- Orthopaedics, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Daniel Li
- Orthopaedics, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Yunlong Ma
- Orthopaedics, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, CHN
| | - Decheng Wu
- Orthopaedics, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, CHN
| | - Yuangzheng Ma
- Orthopaedics, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, CHN
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Abstract
Of the 10 million incident cases of tuberculosis (TB) globally in 2017, around 558,000 cases were rifampicin-resistant of which 82% were multidrug-resistant (MDR) TB. In England, 5,102 cases were recorded of which 55 cases (1.8%) were MDR-TB. MDR-TB cases have worse outcomes and are a serious public health issue.Polymerase chain reaction (PCR) tests allow a faster approach to diagnose TB and predict drug susceptibility. The emerging use of whole genome sequencing may improve the diagnostic workflow compared with standard drug susceptibility testing, with more rapid molecular sensitivity results and more precise contact investigation of linked cases.Treatment of MDR-TB remains a challenge as it relies on prolonged second-line drug treatments that are less effective and more toxic than first-line treatments. Two new drug treatments have been approved; bedaquiline and delamanid. In addition, a shorter treatment regimen of 9-12 months can be considered instead of the conventional 20-24 month regimen.
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Affiliation(s)
- Mirae Park
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust, London, UK
| | | | - Onn Min Kon
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
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Rea B, Maisel JR, Glaser L, Alby K. Identification of Clinically Relevant Mycobacterial Species After Extended Incubation Times in the BACTEC MGIT System. Am J Clin Pathol 2019; 151:63-67. [PMID: 30169764 DOI: 10.1093/ajcp/aqy086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objectives Traditionally, for mycobacterial culture both solid and broth media are used and routinely held for 6 weeks minimum to optimize yield. We retrospectively reviewed all positive mycobacterial cultures over a 12-month period to assess growth kinetics of clinically relevant isolates. Methods From January to December 2015, 658 positive mycobacteria cultures by solid (7H11 and 7H10 plates) and/or broth (BACTEC MGIT) media were identified and reviewed. Results In broth-only cultures, 21 of 153 (13.7%) from 21 patients were positive after 28 days' incubation. Subsequent chart review revealed the following species: 11 Mycobacterium avium intracellulare complex (MAI), five Mycobacterium tuberculosis (MTB), and five other non-MTB/MAI mycobacteria. Two of the cases of MTB were first-time isolates, and 11.4% of MTB-positive cultures became positive after 4 weeks' incubation. Conclusions These data provide strong evidence reaffirming that clinically meaningful results are frequently detected after extended incubation times by broth-only methods, including several MTB isolates.
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Affiliation(s)
- Bryan Rea
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Julia R Maisel
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
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Ismail N, Omar SV, Ismail NA, Peters RPH. In vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants. J Microbiol Methods 2018; 153:1-9. [PMID: 30165087 DOI: 10.1016/j.mimet.2018.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
Abstract
Bedaquiline, clofazimine and linezolid are pertinent drugs for drug-resistant tuberculosis. Drug-resistant mutants provide insight into important resistance acquisition mechanisms. Methods for in vitro Mycobacterium tuberculosis mutant generation are poorly described. Induction (serial passaging) and spontaneous (adapted Luria-Delbrück assay) approaches using M. tuberculosis ATCC reference strains (one fully-susceptible, four unique mono-resistant) were performed. Mutant MIC values were confirmed (MGIT960) and resultant RAVs compared between approaches and to a catalog of previously published RAVs. Mutant MIC values showed a 3-4-fold (induced) and a 1-4-fold (spontaneous) increase compared to baseline. The pyrazinamide-resistant strain had higher baseline MIC values and acquired resistance (≥4-fold) in fewer passages than other strains (induction approach) for bedaquiline. Previously described and novel RAVs in atpE (8 vs. 1) and rv0678 (4 vs. 12) genes were identified in bedaquiline- and clofazimine-resistant mutants. No rv1979c and rv2535c RAVs were identified. Previously described RAVs were identified in rplC and rrl genes for linezolid-resistant mutants. Both approaches successfully led to in vitro mutants with novel RAVs being described in atpE and rv0678 genes. It was observed that pre-existing resistance may influence mutant phenotypic and genotypic characteristics and warrants further attention.
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Affiliation(s)
- N Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa
| | - S V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - N A Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - R P H Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Department of Medical Microbiology, Maastricht University Medical Centre, School CAPHRI, Care and Public Health Research Institute, Maastricht University, Maastricht, the Netherlands.
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Trousil J, Ulmann V, Hrubý M. Fluorescence & bioluminescence in the quest for imaging, probing & analysis of mycobacterial infections. Future Microbiol 2018; 13:933-951. [PMID: 29893148 DOI: 10.2217/fmb-2017-0296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterioses represent a global health problem and rapid diagnostic improvements are urgently required. Mycobacteria-specific fluorescence and bioluminescence phenomena have been found to be useful for a wide range of mycobacteria-focused research. Here, we present a critical survey of the most promising techniques in this field and the potential of new methods under investigation. These approaches include acid-fast staining, intrinsic fluorescence of the coenzyme F420, fluorogenic substrates (e.g., β-lactamase-sensitive coumpounds) and recombination of mycobacteria or mycobacteriophages. Probably the most interesting and emerging host-inspecting approach is in vivo imaging. Detection of fluorescence in vivo, however, is complicated by light scattering, light absorption, and autofluorescence, caused by the tissues. Despite this, many of these systems show promise as the foundations for improved rapid analysis and imaging of mycobacterial infections, both in vitro and in vivo.
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Affiliation(s)
- Jiří Trousil
- Department of Supramolecular Polymer Systems, Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 162 06 Prague 6, Czech Republic.,Department of Analytical Chemistry, Charles University, Faculty of Science, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Vít Ulmann
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health in Ostrava, Partyzánské náměstí 7, 702 00 Ostrava, Czech Republic
| | - Martin Hrubý
- Department of Supramolecular Polymer Systems, Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 162 06 Prague 6, Czech Republic
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Macedo R, Nunes A, Portugal I, Duarte S, Vieira L, Gomes JP. Dissecting whole-genome sequencing-based online tools for predicting resistance in Mycobacterium tuberculosis: can we use them for clinical decision guidance? Tuberculosis (Edinb) 2018; 110:44-51. [PMID: 29779772 DOI: 10.1016/j.tube.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/20/2018] [Accepted: 03/26/2018] [Indexed: 11/30/2022]
Abstract
Whole-genome sequencing (WGS)-based bioinformatics platforms for the rapid prediction of resistance will soon be implemented in the Tuberculosis (TB) laboratory, but their accuracy assessment still needs to be strengthened. Here, we fully-sequenced a total of 54 multidrug-resistant (MDR) and five susceptible TB strains and performed, for the first time, a simultaneous evaluation of the major four free online platforms (TB Profiler, PhyResSE, Mykrobe Predictor and TGS-TB). Overall, the sensitivity of resistance prediction ranged from 84.3% using Mykrobe predictor to 95.2% using TB profiler, while specificity was higher and homogeneous among platforms. TB profiler revealed the best performance robustness (sensitivity, specificity, PPV and NPV above 95%), followed by TGS-TB (all parameters above 90%). We also observed a few discrepancies between phenotype and genotype, where, in some cases, it was possible to pin-point some "candidate" mutations (e.g., in the rpsL promoter region) highlighting the need for their confirmation through mutagenesis assays and potential review of the anti-TB genetic databases. The rampant development of the bioinformatics algorithms and the tremendously reduced time-frame until the clinician may decide for a definitive and most effective treatment will certainly trigger the technological transition where WGS-based bioinformatics platforms could replace phenotypic drug susceptibility testing for TB.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, University of Lisbon, Lisbon, Portugal.
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health, Lisbon, Portugal.
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health, Lisbon, Portugal; Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School, New University of Lisbon, Lisbon, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
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Automated real-time detection of drug-resistant Mycobacterium tuberculosis on a lab-on-a-disc by Recombinase Polymerase Amplification. Anal Biochem 2018; 544:98-107. [DOI: 10.1016/j.ab.2017.12.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/26/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
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Evaluating the diagnostic accuracy of the Xpert MTB/RIF assay on bronchoalveolar lavage fluid: A retrospective study. Int J Infect Dis 2018; 71:14-19. [PMID: 29428408 DOI: 10.1016/j.ijid.2018.01.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Limited data on the diagnostic accuracy of the Xpert MTB/RIF assay using bronchoalveolar lavage fluid from patients with suspected pulmonary tuberculosis (PTB) have been reported in China. Therefore, a retrospective study was designed to evaluate the diagnostic accuracy of this assay. METHODS Clinical, radiological, and microbiological characteristics of 238 patients with suspected PTB were reviewed retrospectively. The sensitivity, specificity, positive predictive value, and negative predictive value for the diagnosis of active PTB were calculated for the Xpert MTB/RIF assay using TB culture or final diagnosis based on clinical and radiological evaluation as the reference standard. RESULTS The sensitivity and specificity of the Xpert MTB/RIF assay were 84.5% and 98.9%, respectively, and those for smear microscopy were 36.2% and 100%, respectively, when compared to the culture method. However, compared with the sensitivity and specificity of final diagnosis based on clinical and radiological evaluation, the sensitivity and specificity of the assay were 72.9% and 98.7%, respectively, which were significantly higher than those for smear microscopy. CONCLUSIONS The Xpert MTB/RIF assay on bronchoalveolar lavage fluid could serve as an additional rapid diagnostic tool for PTB in a high TB-burden country and improve the time to TB treatment initiation in patients with PTB.
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Abstract
Central nervous system (CNS) disease caused by Mycobacterium tuberculosis (MTB) is highly devastating. Tuberculous meningitis (TBM) is the most common form of CNS tuberculosis (TB). Rapid, sensitive, and affordable diagnostic tests are not available. Ziehl-Neelsen (ZN) stain has a very low sensitivity in cases of TBM, the sensitivity rates is of about 10-20%.The detection rate can be improved by taking large volume CSF samples (>6 ml) and prolonged slide examination (30 min). Culture of MTB from the CSF is slow and insufficiently sensitive. The sensitivity is different, which varies from 36% to 81.8%. The microscopic observation drug susceptibility (MODS) assay was recommended by the World Health Organization in 2011. The sensitivity is 65%, which is more sensitive and faster than CSF smear. Commercial PCR assays were found to be insensitive at detecting MTB in CSF samples. Many research provided the value of ADA on the TBM diagnosis. Interferon-gamma release assays (IGRAs) are not recommended for diagnosis of active TB disease. Imaging is essential in diagnosis and showing complications of CNS TB. Thwaites criteria and the Lancet consensus scoring system (LCSS) were developed to improve the diagnosis of TBM. Clinicians will continue to make judgment based on clinical examination, inflammatory CSF examinations, imaging studies, and scoring systems.
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Affiliation(s)
- Yi-Yi Wang
- Department of Neurology, Tianjin Haihe Hospital, Tianjin, P.R. China.
| | - Bing-di Xie
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, P.R. China
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Wang Y, Yu L, Kong X, Sun L. Application of nanodiagnostics in point-of-care tests for infectious diseases. Int J Nanomedicine 2017; 12:4789-4803. [PMID: 28740385 PMCID: PMC5503494 DOI: 10.2147/ijn.s137338] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although tremendous efforts have been put into the treatment of infectious diseases to prevent epidemics and mortality, it is still one of the major health care issues that have a profound impact on humankind. Therefore, the development of specific, sensitive, accurate, rapid, low-cost, and easy-to-use diagnostic tools is still in urgent demand. Nanodiagnostics, defined as the application of nanotechnology to medical diagnostics, can offer many unique opportunities for more successful and efficient diagnosis and treatment for infectious diseases. In this review, we provide an overview of the nanodiagnostics for infectious diseases from nanoparticle-based, nanodevice-based, and point-of-care test (POCT) platforms. Most importantly, emphasis focused on the recent trends in the nanotechnology-based POCT system. The current state-of-the-art and most promising point-of-care nanodiagnostic technologies, including miniaturized diagnostic magnetic resonance platform, magnetic barcode assay system, cell phone-based polarized light microscopy platform, cell phone-based dongle platform, and paper-based POCT platform, for infectious diseases were fully examined. The limitations, challenges, and future trends of the nanodiagnostics in POCTs for infectious diseases are also discussed.
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Affiliation(s)
- Yongzhong Wang
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, Anhui University, Hefei, Anhui, People's Republic of China
| | - Li Yu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Xiaowei Kong
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, Anhui University, Hefei, Anhui, People's Republic of China
| | - Leming Sun
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
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Abraham PR, Pathak N, Pradhan G, Sumanlatha G, Mukhopadhyay S. The N-terminal domain of Mycobacterium tuberculosis PPE17 (Rv1168c) protein plays a dominant role in inducing antibody responses in active TB patients. PLoS One 2017. [PMID: 28651002 PMCID: PMC5484515 DOI: 10.1371/journal.pone.0179965] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The PPE (proline-proline-glutamic acid) proteins of Mycobacterium tuberculosis are characterized by a conserved N-terminal domain of approximately 180 amino acids and variable C-terminal domain. Since last decade, these proteins have gained much importance in the serodiagnosis of tuberculosis (TB) as they act as a source of antigenic variation. We have demonstrated earlier that one of the PPE proteins PPE17 (Rv1168c) induces strong B-cell and T-cell responses in active TB disease and also displays a higher antibody titer compared to immunodominant antigens such as ESAT-6, Hsp60 and PPD. However, the immunodominant domain of PPE17 (N-terminal or C-terminal) was not examined in detail. In the present study, we observed that antibody responses elicited in TB patients were directed mostly towards the N-terminal domain of PPE17 (N-PPE17). The antibody generated against N-PPE17 in TB patients did not significantly cross-react with N-terminal domains of other PPE proteins used in this study. Our data suggest that the N-terminal domain of PPE17 protein is immunodominant and could be used as a better serodiagnostic marker than the full-length PPE17 protein.
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Affiliation(s)
- Philip Raj Abraham
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Niteen Pathak
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Gourango Pradhan
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- Graduate Studies, Manipal University, Manipal, India
| | | | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
- * E-mail: ,
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50
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Atwine D, Orikiriza P, Taremwa I, Ayebare A, Logoose S, Mwanga-Amumpaire J, Jindani A, Bonnet M. Predictors of delayed culture conversion among Ugandan patients. BMC Infect Dis 2017; 17:299. [PMID: 28438118 PMCID: PMC5402635 DOI: 10.1186/s12879-017-2335-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 03/22/2017] [Indexed: 01/10/2023] Open
Abstract
Background Estimates of month-2 culture conversion, a proxy indicator of tuberculosis (TB) treatment efficacy in phase-2 trials can vary by culture-type and geographically with lower rates reported among African sites. The sub-study aimed at comparing TB detection rates of different culture media, within and across rifampicin-based regimens (R10, 15 and 20 mg/Kg) over a 6-month treatment follow-up period, and to establish predictors of month-2 culture non-conversion among HIV-negative TB patients enrolled at RIFATOX trial site in Uganda. Methods Unlike in other Rifatox Trial sites, it is only in Uganda were Lowenstein-Jensen (LJ) and Mycobacteria growth indicator tube (MGIT) were used throughout 6-months for treatment monitoring. Conversion rates were compared at month-2, 4 and 6 across cultures and treatment-type. Binomial regression analysis performed for predictors of month-2 non-conversion. Results Of the 100 enrolled patients, 45% had converted based on combined LJ and MGIT by month-2, with no significant differences across treatment arms, p = 0.721. LJ exhibited higher conversion rates than MGIT at month-2 (58.4% vs 56.0%, p = 0.0707) and month-4 (98.9% vs 88.4%, p = 0.0391) respectively, more so within the high-dose rifampicin arms. All patients had converted by month-6. Time-to-TB detection (TTD) on MGIT and social service jobs independently predict month-2 non-conversion. Conclusion The month-2 culture conversion used in phase 2 clinical trials as surrogate marker of treatment efficacy is influenced by the culture method used for monitoring mycobacterial response to TB treatment. Therefore, multi-centric TB therapeutic trials using early efficacy endpoint should use the same culture method across sites. The Time-to-detection of MTB on MGIT prior to treatment and working in Social service jobs bear an increased risk of culture non-conversion at month-2. Trial registration ISRCTN ISRCTN55670677. Registered 09th November 2010. Retrospectively registered. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2335-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Atwine
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda. .,Mbarara University of Science and Technology, Mbarara, Uganda. .,University of Montpellier 1, Montpellier, France.
| | - Patrick Orikiriza
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda.,Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Taremwa
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda
| | - Arnold Ayebare
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda
| | - Suzan Logoose
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda
| | - Juliet Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda.,Mbarara University of Science and Technology, Mbarara, Uganda
| | | | - Maryline Bonnet
- Epicentre Mbarara Research Centre, PO box 1956, Mbarara, Uganda.,IRD UMI233 TransVIHMI-UM-INSERM U1175, Montpellier, France
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