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Baye N, Atnafu A, Girma S, Belete Y, Yimam S, Getachew B, Ayalew S, Bobosha K, Chanyalew Z, Gize A, Chaniyalew M. Evaluation of molecular and bacteriological detection methods performed on the formalin-fixed paraffin-embedded biopsy samples collected from endometrial and lymph node tuberculosis suspected patients. BMC Infect Dis 2024; 24:1021. [PMID: 39304809 DOI: 10.1186/s12879-024-09908-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Endometrial Tuberculosis is one of the most common gynecological problems known to have serious implications for the quality of life like infertility. The commonly practiced histopathology solely relies on the suggestive feature of Tuberculosis (TB) with low specificity. Regarding the alternative bacteriological and molecular detection tools, little evidence was generated on their utility in the diagnosis of endometrial tuberculosis in Ethiopia. Therefore, we aim to investigate the detection rate of molecular and bacteriological detection methods on formalin-fixed paraffin-embedded biopsy samples for the diagnosis of endometrial and lymph node TB. METHODS A retrospective cross-sectional study was conducted on 90 formalin fixed paraffin embedded biopsy samples from patients with gynecologic and lymph problems collected between 2018 and 2022 at St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia. SPSS version 26 was used for statistical analysis. The diagnostic performance was calculated using the histopathology method as the reference standard. Cohen's Kappa value was used to measure the level of agreement. A test with a P-value of < 0.05 was considered statistically significant. RESULTS A total of 90 samples were analyzed in the current study. Auramine O, GeneXpert MTB/RIF assay, and Real-Time PCR tests have shown a detection rate of 32/90 (36%), 43/90 (47.8%), and 54/90 (60%) respectively (P ≤ 0.01). The sensitivity and specificity of AO were 38.1% and 95% respectively. RT PCR showed superior sensitivity followed by GeneXpert MTB/RIF assay, 70% and 58.6%. AO and molecular methods have shown a similarly low level of agreement with histopathology (Kappa value = 0.2). CONCLUSIONS In a resource-limited setting, the selection of diagnostic tools needs careful attention. Putting the patients on anti-TB treatments based solely on histopathological findings may lead to undesired and adverse complications. Therefore, applying molecular and bacteriological detection methods along with histopathology, could help minimize inappropriate antimicrobial use.
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Affiliation(s)
- Negash Baye
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
- Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.
| | - Abay Atnafu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Selfu Girma
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Yerega Belete
- Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Sofia Yimam
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Sosina Ayalew
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Kidist Bobosha
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Zewditu Chanyalew
- Department of Pathology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Addisu Gize
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Ferrer J, Giménez E, Carretero D, Clari MÁ, Orta N, Navarro D, Albert E. Abbott realtime MTB assay for detecting Mycobacterium tuberculosis complex in respiratory specimens: a cost-benefit analysis. Eur J Clin Microbiol Infect Dis 2024; 43:1699-1709. [PMID: 38958810 DOI: 10.1007/s10096-024-04880-1] [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: 09/19/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
PURPOSE Molecular screening for Mycobacterium tuberculosis (MTB) can lead to rapid empirical treatment inception and reduce hospitalization time and complementary diagnostic tests. However, in low-prevalence settings, the cost-benefit balance remains controversial due to the high cost. METHODS We used a Markov model to perform an economic analysis to evaluate the profit after implementing molecular MTB screening (Period B) compared with conventional culture testing (Period A) in respiratory samples from 7,452 consecutive subjects with presumed tuberculosis (TB). RESULTS The proportion of positivity was comparable between both periods (P > 0.05), with a total of 2.16 and 1.78 samples/patient requested in periods A and B, respectively (P < 0.001). The mean length of hospital stay was 8.66 days (95%CI: 7.63-9.70) in Period B and 11.51 days (95%CI: 10.15-12.87) in Period A (P = 0.001). The healthcare costs associated with diagnosing patients with presumed TB were reduced by €717.95 per patient with PCR screening. The probability of remaining hospitalized and the need for a greater number of outpatient specialty care visits were the variables with the most weight in the model. CONCLUSION Employing PCR as an MTB screening method in a low-prevalence setting may increase the profits to the system.
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Affiliation(s)
- Josep Ferrer
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Diego Carretero
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Mª Ángeles Clari
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Nieves Orta
- Microbiology Unit, Hospital Francisco de Borja, Gandía, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Spain, Av. Blasco Ibáñez 17, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.
- Department of Microbiology, School of Medicine, University of Valencia, Spain, Av. Blasco Ibáñez 17, Valencia, Spain.
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Mohamed A, Lin K, Karabakhtsian R, Chacko K, Bartash R, Liu Q, Meyerowitz E. Molecular diagnosis of an unusual aetiology of chronic abdominal pain with ascites. BMJ Case Rep 2024; 17:e261110. [PMID: 39216897 DOI: 10.1136/bcr-2024-261110] [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: 09/04/2024] Open
Abstract
An immigrant woman in her 60s with a complex medical history and remote occupational exposure to patients with tuberculosis (TB) presented with abdominal pain, early satiety, bloating and weight loss. Physical exam showed abdominal distention and ascites. Diagnostic paracentesis revealed low serum ascites albumin gradient and elevated ascitic lymphocytic count. However, fluid cytology, bacterial and mycobacterial cultures were negative. An interferon-gamma release assay for TB was indeterminate. MRI of the abdomen and pelvis showed a thickened endometrial stripe. Endometrial biopsy demonstrated non-caseating granulomatous endometritis. No organisms were identified on Grocott methenamine silver or acid-fast bacilli special stains. A tissue block from the endometrial biopsy submitted for DNA sequencing was positive for mycobacterium tuberculosis (MTB) complex Urine mycobacterial cultures were obtained and the patient was started on isoniazid, rifampin, ethambutol and pyrazinamide, with significant improvement in her symptoms. Urine mycobacterial cultures were eventually positive for pansusceptible MTB.
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Affiliation(s)
- Anas Mohamed
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ken Lin
- Department of Gynecologic Oncology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rouzan Karabakhtsian
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kristina Chacko
- Department of Transplant Hepatology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rachel Bartash
- Division of Infectious Disease, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qiang Liu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Eric Meyerowitz
- Division of Infectious Disease, Albert Einstein College of Medicine, Bronx, NY, USA
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Segura-Ulate I, Apú N, Cortés B, Querol-Audi J, Zaldívar Y, Ortega CA, Flores-Mora F, Gatica-Arias A, Madrigal-Redondo G. Cross comparison of alternative diagnostic protocols including substitution to the clinical sample, RNA extraction method and nucleic acid amplification technology for COVID-19 diagnosis. Front Mol Biosci 2024; 11:1445142. [PMID: 39247206 PMCID: PMC11377848 DOI: 10.3389/fmolb.2024.1445142] [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: 06/06/2024] [Accepted: 07/31/2024] [Indexed: 09/10/2024] Open
Abstract
Background the gold-standard diagnostic protocol (GSDP) for COVID-19 consists of a nasopharyngeal swab (NPS) sample processed through traditional RNA extraction (TRE) and amplified with retrotranscription quantitative polymerase chain reaction (RT-qPCR). Multiple alternatives were developed to decrease time/cost of GSDP, including alternative clinical samples, RNA extraction methods and nucleic acid amplification. Thus, we carried out a cross comparison of various alternatives methods against GSDP and each other. Methods we tested alternative diagnostic methods using saliva, heat-induced RNA release (HIRR) and a colorimetric retrotranscription loop-mediated isothermal amplification (RT-LAMP) as substitutions to the GSDP. Results RT-LAMP using NPS processed by TRE showed high sensitivity (96%) and specificity (97%), closely matching GSDP. When saliva was processed by TRE and amplified with both RT-LAMP and RT-qPCR, RT-LAMP yielded high diagnostic parameters (88%-96% sensitivity and 95%-100% specificity) compared to RT-qPCR. Nonetheless, when saliva processed by TRE and detected by RT-LAMP was compared against the GSDP, the resulting diagnostic values for sensitivity (78%) and specificity (87%) were somewhat high but still short of those of the GSDP. Finally, saliva processed with HIRR and detected via RT-LAMP was the simplest and fastest method, but its sensitivity against GSDP was too low (56%) for any clinical application. Also, in this last method, the acidity of a large percentage of saliva samples (9%-22%) affected the pH-sensitive colorimetric indicator used in the test, requiring the exclusion of these acidic samples or an extra step for pH correction. Discussion our comparison shows that RT-LAMP technology has diagnostic performance on par with RT-qPCR; likewise, saliva offers the same diagnostic functionality as NPS when subjected to a TRE method. Nonetheless, use of direct saliva after a HIRR and detected with RT-LAMP does not produce an acceptable diagnostic performance.
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Affiliation(s)
- Ismael Segura-Ulate
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Navilla Apú
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Bernal Cortés
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Jordi Querol-Audi
- Laboratorio de Microbiología Experimental y Aplicada (LAMEXA), Universidad de Panamá, Ciudad de Panamá, Panama
- Sistema Nacional de Investigación (SNI), SENACYT, Ciudad de Panamá, Panama
| | - Yamitzel Zaldívar
- Instituto Conmemorativo Gorgas de Estudio de la Salud, Ciudad de Panamá, Panama
| | - Carlos Alexander Ortega
- Sección de Virología, Facultad de Medicina, Universidad de El Salvador, San Salvador, El Salvador
| | - Fernando Flores-Mora
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Andrés Gatica-Arias
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Germán Madrigal-Redondo
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
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Agrawal G, Borody TJ, Aitken JM. Mapping Crohn's Disease Pathogenesis with Mycobacterium paratuberculosis: A Hijacking by a Stealth Pathogen. Dig Dis Sci 2024; 69:2289-2303. [PMID: 38896362 DOI: 10.1007/s10620-024-08508-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) has been implicated in the development of Crohn's disease (CD) for over a century. Similarities have been noted between the (histo)pathological presentation of MAP in ruminants, termed Johne's disease (JD), and appearances in humans with CD. Analyses of disease presentation and pathology suggest a multi-step process occurs that consists of MAP infection, dysbiosis of the gut microbiome, and dietary influences. Each step has a role in the disease development and requires a better understanding to implementing combination therapies, such as antibiotics, vaccination, faecal microbiota transplants (FMT) and dietary plans. To optimise responses, each must be tailored directly to the activity of MAP, otherwise therapies are open to interpretation without microbiological evidence that the organism is present and has been influenced. Microscopy and histopathology enables studies of the mycobacterium in situ and how the associated disease processes manifest in the patient e.g., granulomas, fissuring, etc. The challenge for researchers has been to prove the relationship between MAP and CD with available laboratory tests and methodologies, such as polymerase chain reaction (PCR), MAP-associated DNA sequences and bacteriological culture investigations. These have, so far, been inconclusive in revealing the relationship of MAP in patients with CD. Improved and accurate methods of detection will add to evidence for an infectious aetiology of CD. Specifically, if the bacterial pathogen can be isolated, identified and cultivated, then causal relationships to disease can be confirmed, especially if it is present in human gut tissue. This review discusses how MAP may cause the inflammation seen in CD by relating its known pathogenesis in cattle, and from examples of other mycobacterial infections in humans, and how this would impact upon the difficulties with diagnostic tests for the organism.
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Affiliation(s)
- Gaurav Agrawal
- Division of Diabetes & Nutritional Sciences, King's College London, Franklin-Wilkins Building, London, SE1 9NH, UK.
- , Sydney, Australia.
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Parwati I, Chaidir L, Yunus M, Montain MM, Budhiarko D, Selasih SF, Ristandi RB, Rachman RW, Nurhayati RD, Pambudi I, Budiyati AD. Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia. Front Microbiol 2024; 15:1372647. [PMID: 38800757 PMCID: PMC11123600 DOI: 10.3389/fmicb.2024.1372647] [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: 01/18/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Background Tuberculosis (TB) is one of the major global health issues due to its high mortality rate, especially in low- and middle-income countries. One of the key success points of the TB eradication program is early TB diagnosis, which requires rapid and accurate diagnostic testing. This study aimed to evaluate the performance of a newly developed RT-PCR kit (Indigen MTB/DR-TB RT-PCR) in a routine TB clinical setting. Method A multi-fluorescence RT-PCR assay was designed and developed to detect regions within IS6110, rpoB, katG, and inhA of the Mycobacterium tuberculosis (MTB) genes. Sputum specimens were obtained from suspected TB patients who visited TB healthcare facilities in two major cities of Indonesia from September 2022 to May 2023. Specimens were assessed using Indigen MTB/DR-TB RT-PCR, acid-fast bacillus (AFB) smear microscopy, MTB culture, and drug susceptibility testing (DST) methods. Fisher's exact test (χ2) was used to analyze the Indigen performance relative to culture methods. Result The performance of Indigen MTB/DR-TB RT-PCR to detect MTB was assessed using 610 sputum specimens obtained from suspected patients. The overall sensitivity and specificity were 94.12% (95% CI: 90.86-96.48%) and 98.32% (95% CI: 96.20-99.46%), respectively. When the analysis was performed on AFB smear-negative TB subjects (386 subjects), a lower sensitivity level was found at 78.57% (95% CI: 68.26-86.78%), while the specificity level remained similar at 98.34% (95% CI: 96.18-99.46%). The overall performance of Indigen MTB/DR-TB RT-PCR to detect MTB showed substantial agreement with the MTB culture method (kappa value 0.93). In comparison to DST, the sensitivity and specificity levels of Indigen to detect RIF resistance or INH resistance were 78.2% (95% CI: 61.8-90.2%) and 82.8% (95% CI: 64.2-94.2%), respectively, while the specificity level for both groups was at 100% (95% CI, 87.7-100%). Conclusion Indigen MTB/DR-TB RT-PCR demonstrated reliable performance for TB molecular diagnostic testing and can be implemented in routine TB diagnostic settings.
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Affiliation(s)
- Ida Parwati
- Department of Clinical Pathology, Faculty of Medicine, Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Yunus
- Stem Cell and Cancer Institute, PT. Kalbe Farma, Jakarta, Indonesia
| | - Maya Marinda Montain
- Unit Pelayanan Fungsional Balai Besar Kesehatan Paru Masyarakat Bandung (UPF BBKPM), Bandung, Indonesia
| | - Dini Budhiarko
- Stem Cell and Cancer Institute, PT. Kalbe Farma, Jakarta, Indonesia
| | | | | | | | | | - Imran Pambudi
- Directorate General of Diseases Prevention and Control, Ministry of Health of the Republic of Indonesia, Jakarta, Indonesia
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Chotmongkol V, Kosallavat S, Sawanyawisuth K, Khamsai S, Kasemsap N, Vorasoot N, Kongbunkiat K, Tiamkao S, Chaimanee P. Evaluation of seegene anyplex MTB/NTM real-time detection assay for diagnosis of tuberculous meningitis. Orphanet J Rare Dis 2024; 19:7. [PMID: 38172862 PMCID: PMC10765641 DOI: 10.1186/s13023-023-03009-5] [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: 09/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Tuberculous meningitis (TBM) is a common central nervous system infectious disease. Polymerase chain reaction (PCR) assay is a useful method for the rapid diagnosis of TBM. The Seegene Anyplex MTB/NTM real-time detection assay has good sensitivity and specificity for detection of tuberculosis in respiratory specimens, though, data regarding other specimens are lacking. This study aims to define the diagnostic role of Seegene Anyplex MTB/NTM real-time detection assay in TBM in adults. METHODS This was a retrospective study of 367 adults with symptomatic community acquired meningitis between December 2013 and December 2019. Cerebrospinal fluid (CSF) had been sent for conventional diagnosis, including culture to identify Mycobacterium tuberculosis, and Seegene Anyplex MTB/NTM real-time detection assay. Other diagnostic examinations were performed as necessary. RESULTS Of the 367 patients in the study, 37 were diagnosed with TBM (14 with definite TBM and 23 with probable TBM). Between the total TBM cases (n = 37) and non-TBM cases (n = 330), clinical sensitivity was 32.4% and specificity was 100%, the positive predictive value was 100%, and the negative predictive value was 93.0%. Between the definite TBM cases (n = 14) and non-TBM cases (n = 330), clinical sensitivity was 50.0% and specificity was 100%, the positive predictive value was 100%, and the negative predictive value was 97.9%. CONCLUSION Due to lack of sensitivity, we suggest Seegeen Anyplex MTB/NTM real-time detection assay should not be used to rule out TBM but is useful for definite diagnosis.
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Affiliation(s)
- Verajit Chotmongkol
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Seththawut Kosallavat
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Kittisak Sawanyawisuth
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Sittichai Khamsai
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand.
| | - Narongrit Kasemsap
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Nisa Vorasoot
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Kannikar Kongbunkiat
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Somsak Tiamkao
- Department of Medicine, Faculty of Medicine, Khon Kaen University, 123 Mittraparp Friendship Road, 40002, Khon Kaen, Thailand
| | - Prajuab Chaimanee
- Clinical Laboratory Section, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Park J, Kwak N, Chae JC, Yoon EJ, Jeong SH. A Two-Step Real-Time PCR Method To Identify Mycobacterium tuberculosis Infections and Six Dominant Nontuberculous Mycobacterial Infections from Clinical Specimens. Microbiol Spectr 2023; 11:e0160623. [PMID: 37378523 PMCID: PMC10434164 DOI: 10.1128/spectrum.01606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Tuberculosis (TB) is an ongoing threat to public health, and furthermore, the incidence of infections by nontuberculous mycobacteria (NTM), whose symptoms are not distinguishable from TB, is increasing globally, thus indicating a need for accurate diagnostics for patients with suspected mycobacterial infections. Such diagnostic strategies need to include two steps, (i) detecting the mycobacterial infections and, if the case is an NTM infection, (ii) identifying the causative NTM pathogen. To eliminate a false-positive TB diagnosis for a host vaccinated by the bacillus Calmette-Guérin (BCG) strain of Mycobacterium bovis, a new target specific for M. tuberculosis species was selected, together with the species-specific targets for the six dominant NTM species of clinical importance, i.e., M. intracellulare, M. avium, M. kansasii, M. massiliense, M. abscessus, and M. fortuitum. Using sets of primers and probes, a two-step real-time multiplex PCR method was designed. The diagnostic performance was assessed by using a total of 1,772 clinical specimens from patients with suspected TB or NTM infection. A total of 69.4% of M. tuberculosis and 28.8% of NTM infections were positive for the primary step of the real-time PCR corresponding to the culture within 10 weeks, and mycobacterial species of 75.5% of the NTM-positive cases were identified by the secondary step. The two-step method described herein presented promising results and similar diagnostic sensitivity and specificity to commercially available real-time PCR kits for detecting TB and NTM infections. The method also enabled the identification of mycobacterial species in three-quarters of NTM infection cases, thus providing a better treatment strategy. IMPORTANCE Tuberculosis (TB) is an ongoing threat to public health. In addition, infection by nontuberculous mycobacteria (NTM) is a nonnegligible issue for global public health, with increasing incidences. Since the antimicrobial treatment strategy needs to be differed by the causative pathogen, a rapid and accurate diagnostic method is necessary. In this study, we developed a two-step molecular diagnostic method using clinical specimens of TB and NTM infection-suspected patients. The diagnostic power of the new method using the novel target was similar to the widely used TB detection kit, and, among the NTM-positive specimens, three-quarters of the NTM species were able to be identified. This simple and powerful method will be useful as it is, and it could be applied easily to a point-of-care diagnostic apparatus for better application to patients, especially those living in developing countries.
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Affiliation(s)
- Jungho Park
- Division of Biotechnology, Chongbuk National University, Iksan, South Korea
- BioPark Diagnostics Inc., Seoul, South Korea
| | - Naeun Kwak
- BioPark Diagnostics Inc., Seoul, South Korea
- Department of Biomedical Laboratory Science, College of Software and Digital Healthcare Convergence, Yonsei University MIRAE Campus, Wonju, South Korea
| | - Jong-Chan Chae
- Division of Biotechnology, Chongbuk National University, Iksan, South Korea
| | - Eun-Jeong Yoon
- Division of Antimicrobial Resistance Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheonju, South Korea
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Kadivarian S, Rostamian M, Kooti S, Abiri R, Alvandi A. Diagnostic accuracy of gold nanoparticle combined with molecular method for detection of Mycobacterium tuberculosis: A systematic review and meta-analysis study. SENSING AND BIO-SENSING RESEARCH 2023. [DOI: 10.1016/j.sbsr.2023.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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10
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Integration of cytopathology with molecular tests to improve the lab diagnosis for TBLN suspected patients. PLoS One 2022; 17:e0265499. [PMID: 35358212 PMCID: PMC8970391 DOI: 10.1371/journal.pone.0265499] [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: 11/05/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Tuberculosis lymphadenitis (TBLN) diagnosis is often challenging in most resource poor settings. Often cytopathologic diagnosis of TBLN suspected patients is inconclusive impeding timely clinical management of TBLN suspected patients, further exposing suspected patients either for unnecessary use of antibiotics or empirical treatment. This may lead to inappropriate treatment outcome or more suffering of suspected patients from the disease. In this study, an integrated diagnostic approach has been evaluated to elucidate its utility in the identification of TBLN suspected patients. Methods A cross-sectional study was conducted on 96 clinically diagnosed TBLN suspected patients, where fine needle aspirate (FNA) samples were collected at the time of diagnosis. FNA cytology, Ziehl-Neelsen (ZN), Auramine O (AO) staining, GeneXpert MTB/RIF and Real time PCR (RT-PCR) were performed on concentrated FNA samples. Considering culture as a gold standard, the sensitivity, specificity, positive and negative predictive values were calculated. Cohen’s Kappa value was used to measure interrater variability and level of agreement and a P-value of <0.05 was considered as statistically significant. Result Out of the 96 FNA sample, 12 (12.5%) were identified to have Mycobacterium tuberculosis (Mtb) using ZN staining, 27 (28.1%) using AO staining, 51 (53.2%) using FNAC, 43 (44.7%) using GeneXpert MTB/RIF, 51 (53.1%) using Real time PCR (RT-PCR) and 36 (37.5%) using Lowenstein-Jensen (LJ) culture. Compared to LJ culture, the sensitivities of GeneXpert MTB/RIF, RT-PCR, and FNAC were 91.7%, 97.2%, and 97.2%, respectively and the specificities were 83.3%, 73.3%, and 68.3%, respectively. GeneXpert MTB/RIF and RT-PCR when combined with FNAC detected 61 (63.5%) cases as having Mtb, and the sensitivity and specificity was 100% and 58.3%, respectively. Conclusion FNA cytology and RT-PCR detected more TBLN cases compared to other Mtb detection tools and the detection sensitivity even improved when FNA cytology was combined with GeneXpert MTB/RIF, performed on concentrated FNA sample, suggesting the combined tests as an alternative approach for improved diagnosis of TBLN.
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Malinis M, LaHoz RM, Vece G, Annambhotla P, Aslam S, Basavaraju SV, Bucio J, Danziger-Isakov L, Florescu DF, Jones JM, Rana M, Wolfe CR, Michaels MG. Donor-derived tuberculosis among solid organ transplant recipients in the United States - 2008-2018. Transpl Infect Dis 2022; 24:e13800. [PMID: 35064737 DOI: 10.1111/tid.13800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis can be transmitted via organ donation and result in severe outcomes. To better understand donor-derived tuberculosis (DDTB), all potential transmissions reported to the Organ Procurement and Transplantation Network (OPTN) Ad Hoc Disease Transmission Advisory Committee between 2008-2018 were analyzed. Among 51 total reports, nine (17%) (9 donors/35 recipients) had ≥1 recipient with proven/probable disease transmission. Of these, eight were reported due to recipient disease, and one was reported due to a positive donor result. Proven/probable DDTB transmissions were reported in six lung and five non-lung recipients. The median time to diagnosis was 104 days post-transplant (range 0-165 days). Pulmonary TB, extrapulmonary TB, pulmonary plus extrapulmonary TB, and asymptomatic TB infection with positive interferon-gamma release assay were present in five, three, one, and two recipients, respectively. All recipients received treatment and survived except for one whose death was not attributed to TB. All donors associated with proven/probable DDTB had ≥1 TB risk factor. Six were born in a TB-endemic country, five had traveled to a TB-endemic country, 3 had been incarcerated, and 3 had latent TB infection. These cases highlight the importance of evaluating donors for TB based on risk factors. Early post-transplant TB in organ recipients of donors with TB risk factors requires prompt reporting to OPTN to identify other potential affected recipients and implement timely treatment interventions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maricar Malinis
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Ricardo M LaHoz
- Division of Infectious Disease and Geographic Medicine, University of Texas Southwestern, Dallas, TX
| | | | | | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA
| | | | | | - Lara Danziger-Isakov
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH
| | - Diana F Florescu
- Division of Infectious Diseases, Department of Internal Medicine University of Nebraska Medical Center, Lincoln, NE
| | | | - Meenakshi Rana
- Division of Infectious Diseases, Mount Sinai School of Medicine, New York, NY
| | | | - Marian G Michaels
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh and University of Pittsburgh, Pittsburgh, PA
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12
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de Almeida SM, Santana LB, Jr GG, Kussen GB, Nogueira K. Real-time Polymerase Chain Reaction for Mycobacterium tuberculosis Meningitis is More Sensitive in Patients with HIV Co-Infection. Curr HIV Res 2021; 18:267-276. [PMID: 32368978 DOI: 10.2174/1570162x18666200505083728] [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: 01/13/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculous meningitis (TbM) is the most severe complication of extra pulmonary tuberculosis (Tb). There is a higher frequency of positive cerebrospinal fluid (CSF) cultures for Mycobacterium tuberculosis (MTb) in samples from human immunodeficiency virus (HIV) co-infected patients than in those from HIV-negative patients. We hypothesized that real time PCR assays for MTb (MTb qPCR) using CSF would be more sensitive in HIV co-infected patients owing to a greater MTb burden. The present study aimed to verify the diagnostic performance of MTb qPCR in CSF of TbM patients who either were co-infected with HIV or were HIVnegative. METHODS A total of 334 consecutive participants with suspected TbM were divided into two groups: HIV co-infected and HIV-negative; each group was categorized into definite TbM, probable TbM, possible TbM, and TbM-negative subgroups based on clinical, laboratory and imaging data. We evaluated the diagnostic characteristics of MTb qPCR analysis to detect TbM in CSF by comparing the results to those obtained for definite TbM (i.e., positive MTb culture) and/or probable TbM in CSF, as gold standard. RESULTS The sensitivity of MTb qPCR in the definite and probable subgroups of the HIV coinfected participants (n = 14) was 35.7%, with a specificity of 93.8%, negative predictive value (NPV) of 94.4%, and negative clinical utility index (CUI-) of 0.89. Results of the HIV-negative group (n = 7) showed lower sensitivity (14.3%) and similar specificity, NPV, and CUI-. CONCLUSION The findings confirmed our hypothesis, despite the low sensitivity. MTb qPCR may significantly contribute to diagnosis when associated with clinical criteria and complementary examinations.
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Affiliation(s)
- Sergio M de Almeida
- Neuroinfection Outclinic, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Lucas B Santana
- Neuroinfection Outclinic, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Gilberto Golin Jr
- Neuroinfection Outclinic, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Gislene B Kussen
- Bacteriology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Keite Nogueira
- Bacteriology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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Willemse D, Kaushal D. Using genomic DNA copies to enumerate Mycobacterium tuberculosis load in macaque tissue samples. Tuberculosis (Edinb) 2021; 129:102102. [PMID: 34139570 DOI: 10.1016/j.tube.2021.102102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/30/2021] [Accepted: 06/06/2021] [Indexed: 11/29/2022]
Abstract
It is important to accurately quantify Mycobacterium tuberculosis (Mtb) load in laboratory-based tuberculosis (TB) research. This study aims to determine if real-time quantitative PCR (qPCR) and digital PCR (dPCR) can be used instead of colony forming unit (CFU) enumeration, to quantify Mtb load in rhesus and cynomolgus macaque tissue samples. Tissue samples of actively infected high Mtb-burden rhesus and cynomolgus macaques were selected from historic sample collections. CFUs were enumerated by plating, and Chelex-extracted genomic DNA used to quantify bacterial load by qPCR and dPCR. Three genes, sigA, 16S and CFP10, were assessed for their ability to quantify Mtb. All genes showed comparable quantification of Mtb between 2 and 20 000 copies/μl in the qPCR and 5-4000 copies/μl in the dPCR assay. The highest bacterial load was observed with dPCR, followed by qPCR, and CFU enumeration. Although the CFU count was consistently lower than the genomic copy numbers predicted by qPCR and dPCR, a significant correlation was observed. Quantification of Mtb by PCR was, however, only possible in higher-Mtb-load samples, suggesting that qPCR and dPCR quantification assays can predict bacterial load in actively infected and higher-Mtb-burden macaque tissue samples.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA.
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14
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Development and Validation of Signature Sequence-Based PCR for Improved Molecular Diagnosis of Tuberculosis. J Mol Diagn 2021; 23:1138-1144. [PMID: 34116244 DOI: 10.1016/j.jmoldx.2021.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022] Open
Abstract
Reliable, fast, and affordable diagnosis for tuberculosis (TB) remains a challenge to reduce disease incidence in resource-poor countries. Tests based on nucleotide sequences that are signature to Mycobacterium tuberculosis have the potential to make a positive impact on case detection rates, which can eventually help control TB. Using extensive comparative bioinformatics approach, we mined the genome for M. tuberculosis-specific genes and identified four genes so-called signature sequence (SS). With <25% homology with other known genes/proteins of mycobacterial/nonmycobacterial origin in various databases, these SS genes are ideal targets for species-specific identification. Sputum from suspected patients was liquefied using novel complete liquefying reagent, and DNA was isolated. Samples from patients (n = 417), reporting to TB clinics at two different hospitals, which met our inclusion criteria, were collected for this study. A small number (n = 143) was used for initial standardization, and the remaining patient samples (n = 274) were evaluated by SS and compared with smear microscopy, GeneXpert, culture, and clinical outcome. An overwhelming sensitivity of 97.0%, significantly higher than GeneXpert (95.0%), was seen. SS could pick all smear-negative, but culture-positive samples, along with other culture-negative samples; some of the latter were declared clinically positive. Our results yielded superior sensitivity and specificity through conventional PCR.
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15
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Takhelmayum U, Daimai N, Laishram K, Juneja N, Yogananda ML, Longjam D. A case of postoperative tubercular spondylitis following microdiscectomy for lumbar disc herniation. Surg Neurol Int 2021; 12:265. [PMID: 34221596 PMCID: PMC8247726 DOI: 10.25259/sni_469_2021] [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: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Postoperative infections are one of the most common complications of spine surgery. However, following a lumbar microdiscectomy, a postoperative infection involving Mycobacterium tuberculosis (MTB) is extremely rare. Case Description: One and half months after a L4-5 microdiscectomy, a 47-year-old immunocompromised male with hepatitis B infection presented with low back and bilateral gluteal pain. The MRI revealed a large intraspinal/paraspinal fluid collection spanning from L4 to S1 along with an anterior epidural collection at L5. The patient underwent a L4 lumbar laminectomy for abscess drainage and wound debridement. After obtaining a positive culture for MTB, four antitubercular drug therapies (ATTs) were started, that is, isoniazid (H), rifampicin (R), ethambutol (E), a. One month later, the patient had minimal pain and no residual neurological deficit. Conclusion: MTB infection, although rare, should be considered among the differential diagnoses of postoperative infections following lumbar spine surgery in immunocompromised patients living in areas where tuberculosis is endemic.
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Affiliation(s)
- Umesh Takhelmayum
- Department of Orthopaedics, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
| | - Namjubou Daimai
- Department of Orthopaedics, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
| | - Kanchana Laishram
- Department of Orthopaedics, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
| | - Nikhil Juneja
- Department of Orthopaedics, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
| | - M L Yogananda
- Department of Orthopaedics, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
| | - Deepa Longjam
- Department of Pathology, J. N. Institute of Medical Sciences, Imphal East, Manipur, India
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Bernal-Martínez L, Herrera L, Valero C, de la Cruz P, Ghimpu L, Mesa-Arango AC, Santoni G, Goterris L, Millán R, Buitrago MJ. Differential Diagnosis of Fungal Pneumonias vs. Tuberculosis in AIDS Patients by Using Two New Molecular Methods. J Fungi (Basel) 2021; 7:jof7050336. [PMID: 33925404 PMCID: PMC8145742 DOI: 10.3390/jof7050336] [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: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/30/2022] Open
Abstract
Opportunistic fungal pneumonias (OFP) are the main cause of death in AIDS patients worldwide. Diagnosis of these infections is often late as tuberculosis (TB) is frequently the first suspicion. In addition, diagnostic tools have limitations and are unavailable in disadvantaged regions. To perform the differential diagnosis of the main fungi causing OFP in AIDS patients (Histoplasma capsulatum, Cryptococcus neoformans/C. gattii and Pneumocystis jirovecii) vs. the Mycobacterium tuberculosis complex (MTBC), two new assays were developed: (i) a multiplex real-time PCR (MRT-PCR) and (ii) a simple and cost-effective method based on real-time PCR and the analysis of melting curves after amplification (MC-PCR). Both of the techniques were optimized and standardized “in vitro”, showing a suitable reproducibility (CV ranged between 1.84 and 3.81% and 1.41 and 4.83%, respectively), a 100% specificity and detection limits between 20 and 2 fg of genomic DNA per 20 µL of reaction. A validation study was performed by retrospectively using 42 clinical samples from 37 patients with proven fungal infection or TB, and 33 controls. The overall sensitivity for the MRT-PCR assay and the MC-PCR assay was 88% and 90.4%, respectively. Both techniques were fast, sensitive and reproducible, allowing for the detection of these pathogens and the performance of a differential diagnosis.
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Affiliation(s)
- Leticia Bernal-Martínez
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Laura Herrera
- Centro Nacional de Microbiología, Mycobacteria Unit, Instituto de Salud Carlos III, 28220 Madrid, Spain;
| | - Clara Valero
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Paula de la Cruz
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Larisa Ghimpu
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Ana C. Mesa-Arango
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Gabriela Santoni
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Lidia Goterris
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
| | - Rosario Millán
- Department of Microbiology, Hospital Universitario Puerta de Hierro, 28220 Madrid, Spain;
| | - María José Buitrago
- Centro Nacional de Microbiología, Mycology Reference Laboratory, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain; (L.B.-M.); (C.V.); (P.d.l.C.); (L.G.); (A.C.M.-A.); (G.S.); (L.G.)
- Correspondence:
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17
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Sánchez-Carvajal JM, Galán-Relaño Á, Ruedas-Torres I, Jurado-Martos F, Larenas-Muñoz F, Vera E, Gómez-Gascón L, Cardoso-Toset F, Rodríguez-Gómez IM, Maldonado A, Carrasco L, Tarradas C, Gómez-Laguna J, Luque I. Real-Time PCR Validation for Mycobacterium tuberculosis Complex Detection Targeting IS 6110 Directly From Bovine Lymph Nodes. Front Vet Sci 2021; 8:643111. [PMID: 33981742 PMCID: PMC8109245 DOI: 10.3389/fvets.2021.643111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/22/2021] [Indexed: 11/25/2022] Open
Abstract
Rapid and accurate diagnostic tools, such as Real-Time PCR (qPCR), need to be implemented as a confirmatory test in the framework of bovine tuberculosis (bTB) surveillance and control programs, shortening the turnaround time to confirm bTB infection. The present study aimed to evaluate a direct qPCR from fresh tissue samples targeting the insertion sequence IS6110 using individually homogenized bovine lymph nodes compared with microbiological culture. Retropharyngeal, tracheobronchial, and mesenteric lymph nodes fresh tissue samples (n = 687) were collected from 230 different cattle carcasses at the slaughterhouse. Only 23 of the 230 examined animals showed tuberculosis-like lesions, with 62 of 230 considered as positive. Among these 62 animals, 61 resulted as culture-positive, whereas 48 were qPCR-positive. Thus, this qPCR targeting IS6110 showed an apparent diagnostic sensitivity and specificity values of 77.1% [95% confidence interval (CI): 66.5–87.6%] and 99.4% (95% CI: 98.3–100.6%), respectively, and a positive predictive value of 97.9% (95% CI: 93.9–102.0%) and negative predictive value of 92.3% (95% CI: 88.4–96.2%). Positive and negative likelihood ratios were 130.2 and 0.2, respectively, and the agreement between microbiological culture and this qPCR was almost perfect (κ = 0.82). These results highlight this qPCR targeting IS6110 as a suitable complementary method to confirm bTB in animals with either tuberculosis-like lesions or non-tuberculosis-like lesions, decreasing the number of samples subjected to microbiological culture and, hence, its overall associated costs and the turnaround time (under 48 h) to confirm bTB infection. Besides, sampling mesenteric lymph node, which is uncommonly sampled, together with tracheobronchial and retropharyngeal ones, is advisable during postmortem inspection in bTB surveillance programs at the slaughterhouse, especially in areas with a low bTB prevalence scenario.
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Affiliation(s)
| | | | - Inés Ruedas-Torres
- Department of Anatomy and Comparative Pathology and Toxicology, University of Córdoba, Córdoba, Spain
| | | | - Fernanda Larenas-Muñoz
- Department of Anatomy and Comparative Pathology and Toxicology, University of Córdoba, Córdoba, Spain
| | - Eduardo Vera
- Department of Anatomy and Comparative Pathology and Toxicology, University of Córdoba, Córdoba, Spain.,Department of Animal Health, University of Córdoba, Córdoba, Spain
| | | | | | | | | | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, University of Córdoba, Córdoba, Spain
| | - Carmen Tarradas
- Department of Animal Health, University of Córdoba, Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, University of Córdoba, Córdoba, Spain
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Agrawal G, Aitken J, Hamblin H, Collins M, Borody TJ. Putting Crohn's on the MAP: Five Common Questions on the Contribution of Mycobacterium avium subspecies paratuberculosis to the Pathophysiology of Crohn's Disease. Dig Dis Sci 2021; 66:348-358. [PMID: 33089484 PMCID: PMC7577843 DOI: 10.1007/s10620-020-06653-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
For decades, Mycobacterium avium subspecies paratuberculosis (MAP) has been linked to the pathogenesis of Crohn's disease. Despite many investigations and research efforts, there remains no clear unifying explanation of its pathogenicity to humans. Proponents argue Crohn's disease shares many identical features with a granulomatous infection in ruminants termed Johne's disease and similarities with ileo-cecal tuberculosis. Both are caused by species within the Mycobacterium genus. Sceptics assert that since MAP is found in individuals diagnosed with Crohn's disease as well as in healthy population controls, any association with CD is coincidental. This view is supported by the uncertain response of patients to antimicrobial therapy. This report aims to address the controversial aspects of this proposition with information and knowledge gathered from several disciplines, including microbiology and veterinary medicine. The authors hope that this discussion will stimulate further research aimed at confirming or refuting the contribution of MAP to the pathogenesis of Crohn's disease and ultimately lead to advanced targeted clinical therapies.
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Affiliation(s)
- Gaurav Agrawal
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia.
- Guy's and St. Thomas' NHS Foundation Trust & King's College, London, UK.
| | - John Aitken
- Microbiology, Otakaro Pathways, Christchurch, New Zealand
| | - Harrison Hamblin
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia
| | - Michael Collins
- Veterinary Microbiology, Department of Pathobiological Sciences, University of Wisconsin, Madison, USA
| | - Thomas J Borody
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia
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Kim J, Park BG, Lim DH, Jang WS, Nam J, Mihn DC, Lim CS. Development and evaluation of a multiplex loop-mediated isothermal amplification (LAMP) assay for differentiation of Mycobacterium tuberculosis and non-tuberculosis mycobacterium in clinical samples. PLoS One 2021; 16:e0244753. [PMID: 33406154 PMCID: PMC7787462 DOI: 10.1371/journal.pone.0244753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The rapid and accurate diagnosis of tuberculosis (TB) is important to reduce morbidity and mortality rates and risk of transmission. Therefore, molecular detection methods such as a real-time PCR-based assay for Mycobacterium tuberculosis (MTB) have been commonly used for diagnosis of TB. Loop-mediated isothermal amplification (LAMP) assay was believed to be a simple, quick, and cost-effective isothermal nucleic acid amplification diagnostic test for infectious diseases. In this study, we designed an in-house multiplex LAMP assay for the differential detection of MTB and non-tuberculosis mycobacterium (NTM), and evaluated the assay using clinical samples. MATERIAL AND METHODS For the multiplex LAMP assay, two sets of specific primers were designed: the first one was specific for IS6110 genes of MTB, and the second one was universal for rpoB genes of mycobacterium species including NTM. MTB was confirmed with a positive reaction with both primer sets, and NTM was identified with a positive reaction by only the second primer set without a MTB-specific reaction. Total 333 clinical samples were analyzed to evaluate the multiplex LAMP assay. Clinical samples were composed of 195 positive samples (72 MTB and 123NTM) and 138 negative samples. All samples were confirmed positivity or negativity by real-time PCR for MTB and NTM. Analytical sensitivity and specificity were evaluated for the multiplex LAMP assay in comparison with acid fast bacilli staining and the culture method. RESULTS Of 123 NTM samples, 121 were identified as NTM and 72/72 MTB were identified as MTB by the multiplex LAMP assay. False negative reactions were seen only in two NTM positive samples with co-infection of Candida spp. All 138 negative samples were identified as negative for MTB and NTM. Analytical sensitivity of the multiplex LAMP assay was 100% (72/72) for MTB, and 98.4% (121/123) for NTM. And the specificity of assay was 100% (138/138) for all. CONCLUSIONS Our newly designed multiplex LAMP assay for MTB and NTM showed relatively good sensitivity in comparison with previously published data to detect isolated MTB. This multiplex LAMP assay is expected to become a useful tool for detecting and differentiating MTB from NTM rapidly at an acceptable sensitivity.
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Affiliation(s)
- Jeeyong Kim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Borae G. Park
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Da Hye Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Woong Sik Jang
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Do-CiC Mihn
- Department of Diagnostic Immunology, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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20
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Goud KI, Kavitha M, Mahalakshmi A, Vempati R, Alodhayani AA, Mohammed AA, Khan IA. Molecular detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary samples in a hospital-based study. Afr Health Sci 2020; 20:1617-1623. [PMID: 34394222 PMCID: PMC8351870 DOI: 10.4314/ahs.v20i4.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a deadly infectious disease. India contributes to one-third of the global TB burden. However, no studies have been carried out in the Telangana (Hyderabad) population using real-time polymerase chain reaction (RT-PCR). Therefore, the current study evaluated the role of RT-PCR as a rapid and non-invasive test to diagnose TB by testing for pulmonary tuberculosis (PTB) and extrapulmonary tuberculosis (EPTB). MATERIALS AND METHODS This hospital-based study examined 1670 samples (900 EPTB; 770 PTB) comprising tissue (n = 537), peritoneal fluid (n = 420), sputum (n = 166), bronchial fluid (n = 126), cerebrospinal fluid (n = 145), ascetic fluid (n = 76), sputum pus (n = 78), urine (n = 79), and bronchoalveolar fluid (n = 43) samples. DNA from samples was separated using specific isolation kits and subjected to RT-PCR. RESULTS In this study, we enrolled 1670 subjects and categorized 54.4% as females and 45.6% as males. The collected samples were categorized as 48.5% of fluid samples, followed by tissue (32.2%), sputum (9.9%), urine (4.7%), and pus-swab (4.6%). RT-PCR analysis revealed that 4.7% patients were positive for Mtb. Our results revealed that 61% of the affected patients were male and 39% were female. Among the specimen types, tissue samples gave the highest proportion of positive results (36.3%). CONCLUSION The results showed that RT-PCR should be implemented and given top priority in TB diagnosis to save time and facilitate a definitive diagnosis. Tissue samples are highly recommended to screen the Mtb through the technique RTPCR. Future studies should extend the technique to the global population and exome sequencing analysis should be performed to identify TB risk markers.
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Affiliation(s)
- Kalal Iravathy Goud
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Matam Kavitha
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Adi Mahalakshmi
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Ravi Vempati
- Molecular Biology and Cytogenetics Department, Apollo Hospitals, Jubilee Hills Hyderabad-500096, Telangana, India
| | - Abdulaziz A Alodhayani
- Family & Community Medicine Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arif A Mohammed
- Center of Excellence in Biotechnology Research, King Saud University, PO Box-2455, Riyadh, Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box-10219, Riyadh-11433, Saudi Arabia
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Sua LF, Bolaños JE, Maya J, Sánchez A, Medina G, Zúñiga-Restrepo V, Fernández-Trujillo L. Detection of mycobacteria in paraffin-embedded Ziehl-Neelsen-Stained tissues using digital pathology. Tuberculosis (Edinb) 2020; 126:102025. [PMID: 33254011 DOI: 10.1016/j.tube.2020.102025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Early diagnosis of paucibacillary tuberculosis represents a challenge, even with direct tissue examination. Digital pathology allows the digital analysis of tissues to identify microorganisms. We aim to develop a program to detect and quantify typical and atypical mycobacteria in paraffin-embedded Ziehl-Neelsen-stained tissues. MATERIAL AND METHODS Program development: The building of the program, named Pat-Scan, included pathology, systems engineering, and scientific applications. The iScan Coreo Au scanner® was used, and 9 variables were adjusted. Ten Ziehl-Neelsen-stained samples were fragmented into 2000 images and analyzed to validate the reproducibility of the bacilli images in the tissue, as detected by the software. RESULTS Pat-Scan included software and a scanner that were used to detect and quantify bacilli in paraffin-embedded Ziehl-Neelsen-stained tissues. All samples containing mycobacteria were successfully analyzed by the scanner, and the bacilli could be detected; these results were validated by expert pathologists by microscopy examination, and the presence of bacilli was confirmed in all cases. CONCLUSIONS Pat-Scan allowed the identification and quantification of mycobacteria in paraffin-embedded Ziehl-Neelsen-stained tissues, offering a reproducible diagnostic method that reduces the time for diagnosis and does not affect precision. Further validation is needed for application in the clinical setting.
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Affiliation(s)
- Luz F Sua
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, Cali, Colombia; Faculty of Health Sciences, Universidad Icesi, Cali, Colombia
| | - John E Bolaños
- Faculty of Health Sciences, Universidad Icesi, Cali, Colombia
| | - Juliana Maya
- Faculty of Health Sciences, Universidad Icesi, Cali, Colombia
| | - Aura Sánchez
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, Cali, Colombia
| | - Giovanna Medina
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, Cali, Colombia
| | | | - Liliana Fernández-Trujillo
- Faculty of Health Sciences, Universidad Icesi, Cali, Colombia; Department of Internal Medicine, Pulmonology Service, Interventional Pulmonology, Fundación Valle del Lil, Cali, Colombia.
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22
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Abdelsadek HA, Sobhy HM, Mohamed KF, Hekal SHA, Dapgh AN, Hakim AS. Multidrug-resistant strains of Mycobacterium complex species in Egyptian farm animals, veterinarians, and farm and abattoir workers. Vet World 2020; 13:2150-2155. [PMID: 33281349 PMCID: PMC7704298 DOI: 10.14202/vetworld.2020.2150-2155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Mycobacterium tuberculosis complex (MTBC) is a group of mycobacteria that are important human pathogens. Mycobacterium tuberculosis and Mycobacterium bovis cause serious chronic life-threatening disease and also significant economic losses in both production and remedication. Recently, emergence of multidrug-resistant tuberculosis (MDR-TB) complex has generated global recognition of the need for rapid and sensitive diagnosis and development of new treatments. The current study illustrates the isolation/identification of MTBC strains in specimens obtained from cows and humans by conventional and real-time polymerase chain reaction (RT-PCR) techniques. Further, the study assesses sensitivity to antituberculosis drugs in isolated MDR strains. Materials and Methods: A total of 1464 samples from cattle (1285 raw milk and 179 lymph node), and 149 human sputum samples, were collected from farms and abattoirs in Delta Egypt. Conventional methods (culture and Ziehl–Neelsen staining) were implemented as were RT-PCR using MTBC universal DNA. The effect of some antituberculosis drugs on obtained isolates was assayed using drug susceptibility proportion and qualitative suspension techniques. Results: The MBTC detection rate using the culture method was higher than for Ziehl–Neelsen staining; raw cow milk (2.56 vs. 1.63%), lymph nodes (51.59 vs. 48.04%), and human sputum (5.36 vs. 4.02%). A total of 135 isolates were obtained. Application of RT-PCR detected 138 isolates from the same set of samples. MBTC isolates were resistant to first-line antituberculosis drugs, such as pyrazinamide, isoniazid, rifampicin, and ethambutol by 78.5, 59.3, 40.7, and 31.8%, respectively, and could be highly resistant to kanamycin (82.3%) and amikacin (80.7%). However, isolates remained sensitive to ciprofloxacin (71.1%) and clarithromycin (73.3%) as second-line drugs. Conclusion: There is a growing risk for isolation of MDR-TB from raw milk and lymph nodes of field tuberculin positive cattle as well as sputum of veterinarians and workers existed in farms and abattoirs. PCR-based techniques have become the gold standard for the identification of mycobacterial species, showing high efficiency compared to bacteriological and microscopic examination. Application of the first- and second-line antituberculosis drugs in combination could counter the MDR-TB concern once infections are identified.
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Affiliation(s)
- Hossam A Abdelsadek
- Central Administration of Veterinary Quarantine, General Organization for Veterinary Services, Dokki, Giza, Egypt
| | - Hassan M Sobhy
- Department of Natural Resources, Faculty of African Postgraduate Studies, Cairo University, Cairo, Egypt
| | - Kh F Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - Sahar H A Hekal
- Department of Natural Resources, Faculty of African Postgraduate Studies, Cairo University, Cairo, Egypt
| | - Amany N Dapgh
- Department of Bacteriology, Animal Health Research Institute, Dokki, Giza, Egypt
| | - Ashraf S Hakim
- Department of Microbiology and Immunology, National Research Centre, Dokki, Cairo, Egypt
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23
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Lee Y, Raviglione MC, Flahault A. Use of Digital Technology to Enhance Tuberculosis Control: Scoping Review. J Med Internet Res 2020; 22:e15727. [PMID: 32053111 PMCID: PMC7055857 DOI: 10.2196/15727] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background Tuberculosis (TB) is the leading cause of death from a single infectious agent, with around 1.5 million deaths reported in 2018, and is a major contributor to suffering worldwide, with an estimated 10 million new cases every year. In the context of the World Health Organization’s End TB strategy and the quest for digital innovations, there is a need to understand what is happening around the world regarding research into the use of digital technology for better TB care and control. Objective The purpose of this scoping review was to summarize the state of research on the use of digital technology to enhance TB care and control. This study provides an overview of publications covering this subject and answers 3 main questions: (1) to what extent has the issue been addressed in the scientific literature between January 2016 and March 2019, (2) which countries have been investing in research in this field, and (3) what digital technologies were used? Methods A Web-based search was conducted on PubMed and Web of Science. Studies that describe the use of digital technology with specific reference to keywords such as TB, digital health, eHealth, and mHealth were included. Data from selected studies were synthesized into 4 functions using narrative and graphical methods. Such digital health interventions were categorized based on 2 classifications, one by function and the other by targeted user. Results A total of 145 relevant studies were identified out of the 1005 published between January 2016 and March 2019. Overall, 72.4% (105/145) of the research focused on patient care and 20.7% (30/145) on surveillance and monitoring. Other programmatic functions 4.8% (7/145) and electronic learning 2.1% (3/145) were less frequently studied. Most digital health technologies used for patient care included primarily diagnostic 59.4% (63/106) and treatment adherence tools 40.6% (43/106). On the basis of the second type of classification, 107 studies targeted health care providers (107/145, 73.8%), 20 studies targeted clients (20/145, 13.8%), 17 dealt with data services (17/145, 11.7%), and 1 study was on the health system or resource management. The first authors’ affiliations were mainly from 3 countries: the United States (30/145 studies, 20.7%), China (20/145 studies, 13.8%), and India (17/145 studies, 11.7%). The researchers from the United States conducted their research both domestically and abroad, whereas researchers from China and India conducted all studies domestically. Conclusions The majority of research conducted between January 2016 and March 2019 on digital interventions for TB focused on diagnostic tools and treatment adherence technologies, such as video-observed therapy and SMS. Only a few studies addressed interventions for data services and health system or resource management.
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Affiliation(s)
- Yejin Lee
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Global Studies Institute, University of Geneva, Geneva, Switzerland
| | - Mario C Raviglione
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Global Studies Institute, University of Geneva, Geneva, Switzerland.,Centre for Multidisciplinary Research in Health Science (MACH), Università di Milano, Milan, Italy
| | - Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Global Studies Institute, University of Geneva, Geneva, Switzerland
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Borrás R, Martínez V, Vinuesa V, Torres I, Orta N, Clari MÁ, Prat J, Navarro D. Field performance of the Abbott RealTime MTB assay for the diagnosis of extrapulmonary tuberculosis in a low-prevalence setting. Enferm Infecc Microbiol Clin 2019; 38:206-211. [PMID: 31668859 DOI: 10.1016/j.eimc.2019.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/05/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The sensitivities of conventional mycobacterial culture in solid or liquid media and acid-fast bacilli (AFB) smear microscopy for Mycobacterium tuberculosis complex (MTBC) detection in extrapulmonary specimens are suboptimal. We evaluated the field performance of the Abbott RealTime MTB assay for the diagnosis of extrapulmonary tuberculosis in a low-prevalence setting. METHODS The total number of extrapulmonary specimens with mycobacterial culture and PCR results was 566: sterile fluids (n=278), non-sterile fluids (n=147), lymph node material (n=69) tissue biopsies (n=63), and abscess aspirates (n=9). A composite standard consisting of mycobacterial culture results, clinical treatment response to anti-TB drugs, when administered, and histopathology, radiological and laboratory findings were used as a reference for sensitivity and specificity calculations. RESULTS Mycobacterial cultures and PCR were positive in 17 and 28 specimens, respectively. The overall agreement between culture and PCR was moderate (Cohen's kappa coefficient: 0.549; P=0.0001). Taking as a reference our composite standard, the sensitivity of the Abbott PCR assay was 77.7%, the specificity 99.5%, the PPV 95.4%, and the NPV 98.8%. In turn, the sensitivity of the mycobacterial culture was 62.9%, the specificity and PPV 100%, and the NPV 97.9%. CONCLUSION The good field performance of the Abbott RealTime MTB assay makes it valuable for the diagnosis of extrapulmonary tuberculosis in a low-prevalence setting. The use of molecular methods along with culture improves the diagnosis of extrapulmonary tuberculosis.
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Affiliation(s)
- Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Víctor Martínez
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - Víctor Vinuesa
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - Nieves Orta
- Microbiology Unit, Hospital Francisco de Borja, Gandía, Spain
| | | | - Josep Prat
- Microbiology Unit, Hospital de Sagunto, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain.
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25
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Gompertz M, Carreño L, Gil La Rotta L. Rectal tuberculosis: An uncommon clinical presentation and differential diagnosis with Crohn's disease. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO (ENGLISH EDITION) 2019. [DOI: 10.1016/j.rgmxen.2018.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Rectal tuberculosis: An uncommon clinical presentation and differential diagnosis with Crohn's disease. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2019; 84:524-526. [PMID: 31174906 DOI: 10.1016/j.rgmx.2018.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/14/2018] [Accepted: 12/12/2018] [Indexed: 02/07/2023]
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27
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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de Almeida SM, Borges CM, Santana LB, Golin G, Correa L, Kussen GB, Nogueira K. Validation of Mycobacterium tuberculosis real-time polymerase chain reaction for diagnosis of tuberculous meningitis using cerebrospinal fluid samples: a pilot study. ACTA ACUST UNITED AC 2018; 57:556-564. [DOI: 10.1515/cclm-2018-0524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/17/2018] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Timely diagnosis of tuberculous meningitis (TBM) remains challenging. Molecular diagnostic tools are necessary, particularly in low- and middle-income countries. There is no approved commercial polymerase chain reaction (PCR) assay that can be used to detect Mycobacterium tuberculosis in non-respiratory samples, such as the cerebrospinal fluid (CSF). We aimed to validate the threshold cycle (Ct) cut-off points; calculate the operational characteristics of real-time PCR for detection of M. tuberculosis (MTb qPCR) in the CSF; and the inhibitory affect of CSF red blood cells (RBC) and total proteins on MTb qPCR.
Methods
A total of 334 consecutive participants were enrolled. Based on clinical, laboratory and imaging data, cases of suspected TBM were categorized as definite, probable, possible or not TBM cases. Receiver operating characteristic curve analysis was used to select the best discriminating Ct value.
Results
For TBM cases categorized as definite or probable (n=21), the Ct validated for CSF (≤39.5) improved the diagnostic performance of MTb qPCR on CSF samples. The sensitivity was 29%, specificity was 95%, positive predictive value was 26%, negative predictive value was 95%, efficiency was 90% and positive likelihood was 5.3. The CSF RBC and total protein did not affect the positivity of the MTb qPCR.
Conclusions
These data support the validation of a highly specific but low sensitive MTb qPCR assay for the TBM diagnosis using CSF samples. MTb qPCR contributes significantly to the diagnosis, mainly when associated with conventional microbiology tests and clinical algorithms.
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Affiliation(s)
- Sérgio M. de Almeida
- Hospital de Clínicas-UFPR, Seção de Virologia, Setor Análises Clínicas , Rua Padre Camargo, 280 , Curitiba, PR, 80060-240 , Brazil
- Neuroinfection Outclinic, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
- Virology Laboratory, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe , Curitiba, Paraná , Brazil , Phone/Fax: +55 (41) 3360-7974
| | - Conrado M. Borges
- Neuroinfection Outclinic, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
| | - Lucas B. Santana
- Neuroinfection Outclinic, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
| | - Gilberto Golin
- Neuroinfection Outclinic, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
| | - Lísia Correa
- Bacteriology Laboratory, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
| | - Gislene B. Kussen
- Bacteriology Laboratory, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
| | - Keite Nogueira
- Bacteriology Laboratory, Hospital de Clinicas , Universidade Federal do Paraná , Curitiba, Paraná , Brazil
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Yi Z, Gao K, Li R, Fu Y. Dysregulated circRNAs in plasma from active tuberculosis patients. J Cell Mol Med 2018; 22:4076-4084. [PMID: 29961269 PMCID: PMC6111852 DOI: 10.1111/jcmm.13684] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/11/2018] [Indexed: 02/05/2023] Open
Abstract
Endogenous circular RNAs (circRNAs) have been reported in various diseases. However, their role in active TB remains unknown. The study was aimed to determine plasma circRNA expression profile to characterize potential biomarker and improve our understanding of active TB pathogenesis. CircRNA expression profiles were screened by circRNA microarrays in active TB plasma samples. Dysregulated circRNAs were then verified by qRT-PCR. CircRNA targets were predicted based on analysis of circRNA-miRNA-mRNA interaction. GO and KEGG pathway analyses were used to predict the function of circRNA. ROC curve was calculated to evaluate diagnostic value for active TB. A total of 75 circRNAs were significantly dysregulated in active TB plasma. By further validation, hsa_circRNA_103571 exhibited significant decrease in active TB patients and showed potential interaction with active TB-related miRNAs such as miR-29a and miR-16. Bioinformatics analysis revealed that hsa_circRNA_103571 was primarily involved in ras signalling pathway, regulation of actin cytoskeleton, T- and B-cell receptor signalling pathway. ROC curve analysis suggested that hsa_circRNA_103571 had significant value for active TB diagnosis. Circulating circRNA dysregulation may play a role in active TB pathogenesis. Hsa_circRNA_103571 may be served as a potential biomarker for active TB diagnosis, and hsa_circRNA_103571-miRNA-mRNA interaction may provide some novel mechanism for active TB.
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Affiliation(s)
- Zhengjun Yi
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Kunshan Gao
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China
| | - Ruifang Li
- Department of Medical Microbiology of Clinical Medicine College, Weifang Medical University, Weifang, China
| | - Yurong Fu
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnostics in Universities of Shandong, Weifang Medical University, Weifang, China.,Department of Medical Microbiology of Clinical Medicine College, Weifang Medical University, Weifang, China
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