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Nijiati M, Guo L, Tuersun A, Damola M, Abulizi A, Dong J, Xia L, Hong K, Zou X. Deep learning on longitudinal CT scans: automated prediction of treatment outcomes in hospitalized tuberculosis patients. iScience 2023; 26:108326. [PMID: 37965132 PMCID: PMC10641748 DOI: 10.1016/j.isci.2023.108326] [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: 05/14/2023] [Revised: 08/17/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
Three deep learning (DL)-based prediction models (PMs) using longitudinal CT images were developed to predict tuberculosis (TB) treatment outcomes. The internal dataset consists of 493 bacteriologically confirmed TB patients who completed the anti-tuberculosis treatment with three-time CT scans, including a pretreatment CT scan and two follow-up CT scans. PM1 was trained using only pretreatment CT scans, and PM2 and PM3 were developed by adding follow-up scans. An independent testing was performed on external dataset comprising 86 TB patients. The area under the curve for classifying success and drug-resistant (DR)-TB was improved on both internal (0.609 vs. 0.625 vs. 0.815) and external (0.627 vs. 0.705 vs. 0.735) dataset by adding follow-up scans. The accuracy and F1-score also showed an increasing tendency in the external test. Regular follow-up CT scans can aid in the treatment prediction, and special attention should be given to early intensive phase of treatment to identify high-risk DR-TB patients.
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Affiliation(s)
- Mayidili Nijiati
- Department of Radiology, The First People’s Hospital of Kashi Prefecture, Kashi, China
| | - Lin Guo
- Shenzhen Zhiying Medical Imaging, Shenzhen, China
| | - Abudouresuli Tuersun
- Department of Radiology, The First People’s Hospital of Kashi Prefecture, Kashi, China
| | - Maihemitijiang Damola
- Department of Radiology, The First People’s Hospital of Kashi Prefecture, Kashi, China
| | | | - Jiake Dong
- Department of Radiology, The First People’s Hospital of Kashi Prefecture, Kashi, China
| | - Li Xia
- Shenzhen Zhiying Medical Imaging, Shenzhen, China
| | - Kunlei Hong
- Shenzhen Zhiying Medical Imaging, Shenzhen, China
| | - Xiaoguang Zou
- Clinical Medical Research Center, The First People’s Hospital of Kashi Prefecture, Kashi, China
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Fekadu G, Tolossa T, Turi E, Bekele F, Fetensa G. Pretomanid development and its clinical roles in treating tuberculosis. J Glob Antimicrob Resist 2022; 31:175-184. [PMID: 36087906 DOI: 10.1016/j.jgar.2022.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide. Despite the development of different antituberculosis drugs, managing resistant mycobacteria is still challenging. The discovery of novel drugs and new methods of targeted drug delivery have the potential to improve treatment outcomes, lower the duration of treatment, and reduce adverse events. Following bedaquiline and delamanid, pretomanid is the third medicine approved as part of a novel drug regimen for treating drug-resistant TB. It is a promising drug that has the capacity to shape TB treatment and achieve the End TB strategy set by the World Health Organization. The effectiveness of pretomanid has been reported in different observational and clinical studies. However, long-term safety data in humans are not yet available and the pretomanid-based regimen is recommended under an operational research framework that prohibits its wider and programmatic use. Further research is needed before pretomanid can be celebrated as a promising candidate for the treatment of different categories of TB and specific patients. This review covers the update on pretomanid development and its clinical roles in treating Mycobacterium tuberculosis.
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Affiliation(s)
- Ginenus Fekadu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong; Department of Pharmacy, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia.
| | - Tadesse Tolossa
- Department of Public Health, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Deakin Health Economics, Institute for Health Transformation, Deakin University, Geelong, Victoria
| | - Ebisa Turi
- Department of Public Health, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Deakin Health Economics, Institute for Health Transformation, Deakin University, Geelong, Victoria
| | - Firomsa Bekele
- Department of Pharmacy, College of Health Science, Mattu University, Mattu, Ethiopia
| | - Getahun Fetensa
- Department of Nursing, School of Nursing and Midwifery, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Department of Health behaviour and Society, Faculty of Public Health, Jimma Medical Center, Jimma University, Ethiopia
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Fekadu G, To KKW, You JHS. WITHDRAWN: Pretomanid for the treatment of Mycobacterium tuberculosis: Evidence on the development and clinical roles. J Infect Public Health 2021:S1876-0341(21)00324-5. [PMID: 34742640 DOI: 10.1016/j.jiph.2021.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022] Open
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Ginenus Fekadu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
| | - Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
| | - Joyce H S You
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
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Mnyambwa NP, Mahende C, Wilfred A, Sandi E, Mgina N, Lubinza C, Kahwa A, Petrucka P, Mfinanga S, Ngadaya E, Kimaro G. Antibiotic Susceptibility Patterns of Bacterial Isolates from Routine Clinical Specimens from Referral Hospitals in Tanzania: A Prospective Hospital-Based Observational Study. Infect Drug Resist 2021; 14:869-878. [PMID: 33688222 PMCID: PMC7937390 DOI: 10.2147/idr.s294575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Introduction Antimicrobial resistance is one of the biggest threats of modern public health. Although sub-Saharan Africa is highly burdened with infectious diseases, current data on antimicrobial resistance are sparse. Methods A prospective study was conducted between October 2018 and September 2019 to assess the antibiotic susceptibility patterns of clinical bacterial isolates obtained from four referral hospitals in Tanzania. We used standard media and Kirby-Bauer disc diffusion methods as per Clinical and Laboratory Standards Institute (CLSI) standards. Results We processed a total of 2620 specimens of which 388 (14.8%) were culture-positive from patients with a median (IQR) age of 28 (12–44) years. Of the positive cultures, 52.3% (203) were from females. Most collected specimens were ear pus 28.6% (111), urine 24.0% (93), wound pus 20.6% (80), stool 14.9% (58), and blood 8.3% (32). Predominant isolates were S. aureus 28.4% (110), E. coli 15.2% (59), P. aeruginosa 10.6% (41), P. mirabilis 7.0% (27), V. cholerae 01 Ogawa 6.2% (24), Klebsiella spp. 5.2% (20) and Streptococcus spp. 4.6% (18). Generally, the isolates exhibited a high level of resistance to commonly used antibiotics such as Ampicillin, Amoxicillin-Clavulanic acid, Erythromycin, Gentamicin, Tetracycline, Trimethoprim, third-generation Cephalosporins (Ceftriaxone and Ceftazidime), and reserved drugs (Clindamycin and Meropenem). S. aureus isolates were resistant to most of the antibiotics tested; 66.7% were classified as MRSA infections. Conclusion Antibiotic resistance to commonly prescribed antibiotics was alarmingly high. Our findings emphasize the need for comprehensive national control programs to combat antibiotic resistance.
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Affiliation(s)
- Nicholaus P Mnyambwa
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Coline Mahende
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Amani Wilfred
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Erica Sandi
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Nicodem Mgina
- Central Tuberculosis Reference Laboratory (CTRL), Dar es Salaam, Tanzania
| | - Clara Lubinza
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Amos Kahwa
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Pammla Petrucka
- School of Life Science and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,University of Saskatchewan, Saskatoon, Canada
| | - Sayoki Mfinanga
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania.,School of Life Science and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,Department of Epidemiology and Statistics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Esther Ngadaya
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
| | - Godfather Kimaro
- National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania
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Lai LY, Hsu LY, Weng SH, Chung SE, Ke HE, Lin TL, Hsieh PF, Lee WT, Tsai HY, Lin WH, Jou R, Wang JT. A Glutamine Insertion at Codon 432 of RpoB Confers Rifampicin Resistance in Mycobacterium tuberculosis. Front Microbiol 2020; 11:583194. [PMID: 33193223 PMCID: PMC7604305 DOI: 10.3389/fmicb.2020.583194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious respiratory disease caused by Mycobacterium tuberculosis and one of the top 10 causes of death worldwide. Treating TB is challenging; successful treatment requires a long course of multiple antibiotics. Rifampicin (RIF) is a first-line drug for treating TB, and the development of RIF-resistant M. tuberculosis makes treatment even more difficult. To determine the mechanism of RIF resistance in these strains, we searched for novel mutations by sequencing. Four isolates, CDC-1, CDC-2, CDC-3, and CDC-4, had high-level RIF resistance and unique mutations encoding RpoB G158R, RpoB V168A, RpoB S188P, and RpoB Q432insQ, respectively. To evaluate their correlation with RIF resistance, plasmids carrying rpoB genes encoding these mutant proteins were transfected into the H37Rv reference strain. The plasmid complementation of RpoB indicated that G158R, V168A, and S188P did not affect the MIC of RIF. However, the MIC of RIF was increased in H37Rv carrying RpoB Q432insQ. To confirm the correlation between RIF resistance and Q432insQ, we cloned an rpoB fragment carrying the insertion (encoding RpoB Q432insQ) into H37Rv by homologous recombination using a suicide vector. All replacement mutants expressing RpoB Q432insQ were resistant to RIF (MIC > 1 mg/L). These results indicate that RpoB Q432insQ causes RIF resistance in M. tuberculosis.
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Affiliation(s)
- Li-Yin Lai
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Yu Hsu
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shang-Hui Weng
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shuo-En Chung
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hui-En Ke
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Fang Hsieh
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Ting Lee
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan.,Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan
| | - Hsing-Yuan Tsai
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan.,Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan
| | - Wan-Hsuan Lin
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan.,Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan.,Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare of Taiwan, Taipei, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Mnyambwa NP, Kim DJ, Ngadaya E, Chun J, Ha SM, Petrucka P, Addo KK, Kazwala RR, Mfinanga SG. Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania. Int J Infect Dis 2018; 71:82-88. [DOI: 10.1016/j.ijid.2018.04.796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 01/29/2023] Open
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Mnyambwa NP, Ngadaya ES, Kimaro G, Kim DJ, Kazwala R, Petrucka P, Mfinanga SG. Assessment of sputum smear-positive but culture-negative results among newly diagnosed pulmonary tuberculosis patients in Tanzania. Int J Gen Med 2017; 10:199-205. [PMID: 28744153 PMCID: PMC5513826 DOI: 10.2147/ijgm.s137469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Diagnosis of pulmonary tuberculosis (TB) in technology-limited countries is widely achieved by smear microscopy, which has limited sensitivity and specificity. The frequency and clinical implication of smear-positive but culture-negative among presumptive TB patients remains unclear. A cross-sectional substudy was conducted which aimed to identify the proportion of nontuberculous mycobacteria (NTM) infections among 94 “smear-positive culture-negative” patients diagnosed between January 2013 and June 2016 in selected health facilities in Tanzania. Out of 94 sputa, 25 (26.60%) were GeneXpert® mycobacteria TB positive and 11/94 (11.70%) repeat-culture positive; 5 were Capilia TB-Neo positive and confirmed by GenoType MTBC to be Mycobacterium tuberculosis/Mycobacterium canettii. The remaining 6 Capilia TB-Neo negative samples were genotyped by GenoType® CM/AS, identifying 3 (3.19%) NTM, 2 Gram positive bacteria, and 1 isolate testing negative, together, making a total of 6/94 (6.38%) confirmed false smear-positives. Twenty-eight (29.79%) were confirmed TB cases, while 60 (63.83%) remained unconfirmed cases. Out of 6 (6.38%) patients who were HIV positive, 2 patients were possibly coinfected with mycobacteria. The isolation of NTM and other bacteria among smear-positive culture-negative samples and the presence of over two third of unconfirmed TB cases emphasize the need of both advanced differential TB diagnostic techniques and good clinical laboratory practices to avoid unnecessary administration of anti-TB drugs.
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Affiliation(s)
- Nicholaus Peter Mnyambwa
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Esther S Ngadaya
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Godfather Kimaro
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
| | - Dong-Jin Kim
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Rudovick Kazwala
- Department of Veterinary Medicine, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Pammla Petrucka
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,College of Nursing, University of Saskatchewan, Saskatoon, Canada
| | - Sayoki G Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Center, Dar es Salaam, Tanzania
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