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Mousavi-Sagharchi SMA, Afrazeh E, Seyyedian-Nikjeh SF, Meskini M, Doroud D, Siadat SD. New insight in molecular detection of Mycobacterium tuberculosis. AMB Express 2024; 14:74. [PMID: 38907086 PMCID: PMC11192714 DOI: 10.1186/s13568-024-01730-3] [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: 11/29/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
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Affiliation(s)
| | - Elina Afrazeh
- Department of Marine Biology, Faculty of Marine Science, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | | | - Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| | - Delaram Doroud
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Danchuk SN, Solomon OE, Kohl TA, Dreyer V, Barilar I, Utpatel C, Niemann S, Soolingen DV, Anthony R, van Ingen J, Michael JS, Behr MA. Challenging the gold standard: the limitations of molecular assays for detection of Mycobacterium tuberculosis heteroresistance. Thorax 2024; 79:670-675. [PMID: 38286614 PMCID: PMC11187393 DOI: 10.1136/thorax-2023-220202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVES Heteroresistant infections are defined as infections in which a mixture of drug-resistant and drug-susceptible populations are present. In Mycobacterium tuberculosis (M. tb), heteroresistance poses a challenge in diagnosis and has been linked with poor treatment outcomes. We compared the analytical sensitivity of molecular methods, such as GeneXpert and whole genome sequencing (WGS) in detecting heteroresistance when compared with the 'gold standard' phenotypic assay: the agar proportion method (APM). METHODS Using two rounds of proficiency surveys with defined monoresistant BCG strains and mixtures of susceptible/resistant M. tb, we determined the limit of detection (LOD) of known resistance associated mutations. RESULTS The LOD for rifampin-R (RIF-R) detection was 1% using APM, 60% using GeneXpert MTB/RIF, 10% using GeneXpert MTB/RIF Ultra and 10% using WGS. While WGS could detect mutations beyond those associated with RIF resistance, the LOD for these other mutations was also 10%. Additionally, we observed instances where laboratories did not report resistance in the majority population, yet the mutations were present in the raw sequence data. CONCLUSION The gold standard APM detects minority resistant populations at a lower proportion than molecular tests. Mycobacterium bovis BCG strains with defined resistance and extracted DNA from M. tb provided concordant results and can serve in quality control of laboratories offering molecular testing for resistance. Further research is required to determine whether the higher LOD of molecular tests is associated with negative treatment outcomes.
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Affiliation(s)
- Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Ori E Solomon
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Ivan Barilar
- German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Stefan Niemann
- Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | | | | | | | - Joy S Michael
- Microbiology, Christian Medical College and Hospital Vellore, Vellore, Tamil Nadu, India
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [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: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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Nie S, Zhang Q, Chen R, Lin L, Li Z, Sun Y, Huang J, Feng Z, Cao X, Ye K, Tang L, Zhou J, Cai G, Chen X. Rapid detection of pathogens of peritoneal dialysis-related peritonitis, especially in patients who have taken antibiotics, using metagenomic next-generation sequencing: a pilot study. Ren Fail 2023; 45:2284229. [PMID: 38031397 PMCID: PMC11001327 DOI: 10.1080/0886022x.2023.2284229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION Peritoneal dialysis (PD)-related peritonitis is a serious complication of PD. Improving the diagnostic rate of peritonitis pathogens may substantially benefit peritonitis patients. METHODS The study was conducted in the People's Liberation Army (PLA) General Hospital from 1 June 2021 to 31 May 2022. Information about peritonitis, culture and metagenomic next-generation sequencing (mNGS) results and so on were collected. Patients were divided into antibiotic-use and antibiotic-free groups. The culture and mNGS results were compared using the paired χ2 test. RESULTS Data from 26 patients with peritonitis were collected. 50% of the patients had used antibiotics before samples were obtained (antibiotic-use group). The positivity rate using culture was 92.3% (12 cases) in the antibiotic-free group and 38.5% (5 cases) in the antibiotic-use group (p = 0.011). However, the positivity rate using mNGS was 92.3% (12 cases) regardless of whether antibiotics were used (p = 1.000). After revising the mNGS results, the positivity rate was 84.6% (11 cases) in both groups (p = 1.000). A significant difference between culture and mNGS results of all groups was observed (p = 0.039). The difference no matter between culture and mNGS (p = 0.016) or between culture and modified mNGS (p = 0.031) of the antibiotic-use group was observed. CONCLUSION For patients with PD-related peritonitis who previously received antibiotics, mNGS is suggested. For other patients, mNGS testing can be performed, but the results should be interpreted with caution. Much more research should be done to identify a powerful and ideal tool to detect pathogens underlying PD-related peritonitis.
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Affiliation(s)
- Sasa Nie
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Qingtao Zhang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Rong Chen
- Department of clinical laboratory, the First Medical Center, Chinese PLA General Hospita, Beijing, China
| | - Li Lin
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Zhenzhen Li
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Yanli Sun
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Jing Huang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Zhe Feng
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Xueying Cao
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Kun Ye
- Department of clinical laboratory, the First Medical Center, Chinese PLA General Hospita, Beijing, China
| | - Li Tang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Jianhui Zhou
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Guangyan Cai
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Xiangmei Chen
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
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Molldrem S, Bagani S, Subrahmanyam V, Permar R, Matsiri O, Caiphus C, Kizito B, Modongo C, Shin SS. Botswana tuberculosis (TB) stakeholders broadly support scaling up next-generation whole genome sequencing: Ethical and practical considerations for Botswana and global health. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002479. [PMID: 37967081 PMCID: PMC10651001 DOI: 10.1371/journal.pgph.0002479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Global health agencies are increasingly promoting the scale-up of next-generation whole genome sequencing (NG-WGS) of pathogens into infectious disease control programs, including for tuberculosis (TB). However, little is known about how stakeholders in low-to-middle income countries (LMICs) understand the ethics, benefits, and risks of these proposals. We conducted a qualitative study in Greater Gaborone, Botswana to learn how TB stakeholders there viewed a potential scale-up of NG-WGS into Botswana's TB program. We conducted 30 interviews and four deliberative dialogues with TB stakeholders based in Greater Gaborone, the country's largest city and capital. We created and showed participants an animated video series about a fictional family that experienced TB diagnosis, treatment, contact tracing, and data uses that were informed by NG-WGS. We analyzed transcripts using reflexive thematic analysis. We found broad support for the scale-up of TB NG-WGS in Botswana, owing to perceived benefits. Support was qualified with statements about ensuring adequate planning, resource-allocation, community and stakeholder engagement, capacity-building, and assessing ethical norms around publishing data. Our results suggest that scaling up NG-WGS for TB in Botswana would be supported by stakeholders there, contingent upon the government and other entities adequately investing in the initiative. These findings are relevant to other LMICs considering scale-ups of NG-WGS and related technologies for infectious diseases and suggest the need for sustained research into the acceptability of pathogen sequencing in other contexts.
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Affiliation(s)
- Stephen Molldrem
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Vishnu Subrahmanyam
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rebecca Permar
- Program for Leadership and Character, Office of Academic Advising, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | | | | | | | | | - Sanghyuk S. Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California, United States of America
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Padane A, Harouna Hamidou Z, Drancourt M, Saad J. CRISPR-Based Detection, Identification and Typing of Mycobacterium tuberculosis Complex Lineages. Microbiol Spectr 2023; 11:e0271722. [PMID: 36602330 PMCID: PMC9927308 DOI: 10.1128/spectrum.02717-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/11/2022] [Indexed: 01/06/2023] Open
Abstract
The polymerase chain reaction (PCR)-based detection of Mycobacterium tuberculosis (M. tuberculosis) complex (MTC) in clinical samples is a first-line approach by which to diagnose tuberculosis in clinical microbiology laboratories. In this study, the genome-wide profiling of 3,156 mycobacterial genomes using Roary determined the CRISPR-csm4 gene as specific for MTB. Real time (RT)-PCR and the PCR-sequencing of CRISPR-csm4, tested on a collection of 20 MTC and 5 nontuberculous mycobacteria, confirmed the 20 MTC isolates, whereas the 5 nontuberculous isolates were not detected. Further, 65 of the leftover clinical samples, including 25 GeneXpert-positive and 40 GeneXpert-negative samples, that were used to evaluate the CRISPR-csm4-MTB assay in the clinical microbiology laboratory setting yielded expected results in every case, further allowing for the identification of the M. tuberculosis Beijing lineage. RT-PCR and the PCR-sequencing of CRISPR-csm4 could be implanted in the clinical microbiology laboratory to complement the currently used assays, with the potential of increasing the specification of the MTC pathogens responsible for tuberculosis. IMPORTANCE The whole-genome sequence comparison of the Mycobacterium tuberculosis complex (MTC) genomic sequences that are available in the NCBI database identified a unique, specific gene to be used directly on clinical diagnostic samples to detect MTC against all species of mycobacteria and to differentiate between MTC species, lineages, and sublineages.
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Affiliation(s)
- A. Padane
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Sénégal
| | - Z. Harouna Hamidou
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - M. Drancourt
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J. Saad
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Dong B, He Z, Li Y, Xu X, Wang C, Zeng J. Improved Conventional and New Approaches in the Diagnosis of Tuberculosis. Front Microbiol 2022; 13:924410. [PMID: 35711765 PMCID: PMC9195135 DOI: 10.3389/fmicb.2022.924410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). Timely diagnosis and effective treatment are essential in the control of TB. Conventional smear microscopy still has low sensitivity and is unable to reveal the drug resistance of this bacterium. The traditional culture-based diagnosis is time-consuming, since usually the results are available after 3–4 weeks. Molecular biology methods fail to differentiate live from dead M. tuberculosis, while diagnostic immunology methods fail to distinguish active from latent TB. In view of these limitations of the existing detection techniques, in addition to the continuous emergence of multidrug-resistant and extensively drug-resistant TB, in recent years there has been an increase in the demand for simple, rapid, accurate and economical point-of-care approaches. This review describes the development, evaluation, and implementation of conventional diagnostic methods for TB and the rapid new approaches for the detection of M. tuberculosis.
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Affiliation(s)
- Baoyu Dong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyue Xu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Robinne S, Saad J, Morsli M, Hamidou ZH, Tazerart F, Drancourt M, Baron SA. Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept. Front Microbiol 2022; 13:753969. [PMID: 35432257 PMCID: PMC9008353 DOI: 10.3389/fmicb.2022.753969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.
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Affiliation(s)
- Simon Robinne
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jamal Saad
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Madjid Morsli
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Zelika Harouna Hamidou
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Fatah Tazerart
- IHU Méditerranée Infection, Marseille, France
- Institut des Sciences Vétérinaires, Université de Blida 1, Blida, Algeria
| | - Michel Drancourt
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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10
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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11
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Anthwal D, Jamwal S, Gupta RK, Singhal R, Verma AK, Bhalla M, Myneedu VP, Sarin R, Choudhary S, Tyagi JS, Haldar S. Direct Molecular Detection of Drug-Resistant Tuberculosis from Transported Bio-Safe Dried Sputum on Filter-Paper. Curr Microbiol 2022; 79:110. [PMID: 35175411 DOI: 10.1007/s00284-022-02780-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 11/27/2022]
Abstract
In 2019, amongst half a million new rifampicin-resistant tuberculosis (TB) cases, 78% were multi drug-resistant TB (MDR-TB). Access to rapid and Universal-Drug susceptibility testing (DST) to patients in remote areas is a major challenge to combat drug-resistant TB. To overcome this challenge, we had recently reported the development of 'TB Concentration & Transport kit' for bio-safe ambient temperature transport of dried sputum on filter-paper (Trans-Filter). The present study was conducted to evaluate the utility of DNA extracted from sputum on Trans-Filter in a Multiplex PCR-based sequencing assay (Mol-DSTseq) for diagnosing drug-resistant TB. The developed Mol-DSTseq assays were standardized on Mycobacterium tuberculosis clinical isolates (n = 98) and further validated on DNA extracted from sputum on Trans-Filter (n = 100). Using phenotypic DST as gold standard, the Mol-DSTseq assay showed 100% (95% Confidence Interval [CI] 79.4-100%) and 73.3% (95% CI 54.1-87.7%) sensitivity for detecting rifampicin and isoniazid resistance with a specificity of 85.1% (95% CI 66.2-95.8%) and 100% (95% CI:82.3-100%), respectively. For fluoroquinolones and aminoglycosides, the Mol-DSTseq assay showed a sensitivity of 78.5% (95% CI 49.2-95.3%) and 66.6% (95% CI 9.4-99.1%) with a specificity of 88.2% (95% CI 72.5-96.7%) and 100% (95% CI 93.1-100%), respectively. The Mol-DSTseq assays exhibited a high concordance of ~ 83-96% (κ value: 0.65-0.81) with phenotypic DST for all drugs. In conclusion, the 'TB Concentration and Transport kit' was compatible with Mol-DSTseq assays and has the potential to provide 'Universal-DST' to patients residing in distant areas in high burden countries, like India for early initiation of anti-tubercular treatment.
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Affiliation(s)
- Divya Anthwal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Shaina Jamwal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kumar Gupta
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Ajoy Kumar Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Rohit Sarin
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Tonk, Rajasthan, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, India.
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12
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van Zyl GU. New Technological Developments in Identification and Monitoring of New and Emerging Infections. ENCYCLOPEDIA OF INFECTION AND IMMUNITY 2022. [PMCID: PMC8291697 DOI: 10.1016/b978-0-12-818731-9.00094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Maladan Y, Krismawati H, Wahyuni T, Tanjung R, Awaludin K, Audah KA, Parikesit AA. The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia. BMC Genomics 2021; 22:844. [PMID: 34802420 PMCID: PMC8607662 DOI: 10.1186/s12864-021-08139-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs. RESULT A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R). CONCLUSIONS The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.
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Affiliation(s)
- Yustinus Maladan
- Center for Papua Health Research and Development, Papua, Indonesia.
| | - Hana Krismawati
- Center for Papua Health Research and Development, Papua, Indonesia
| | - Tri Wahyuni
- Center for Papua Health Research and Development, Papua, Indonesia
| | - Ratna Tanjung
- Center for Papua Health Research and Development, Papua, Indonesia
| | | | | | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, International Institute for Life Sciences (I3L), Jakarta, Indonesia.
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Sánchez-Corrales L, Tovar-Aguirre OL, Galeano-Vanegas NF, Castaño Jiménez PA, Martínez-Vega RA, Maldonado-Londoño CE, Hernández-Botero JS, Siller-López F. Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia. PLoS One 2021; 16:e0258402. [PMID: 34618869 PMCID: PMC8496870 DOI: 10.1371/journal.pone.0258402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/25/2021] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) was the pathogen responsible for the highest number of deaths from infectious diseases in the world, before the arrival of the COVID-19 pandemic. Whole genome sequencing (WGS) has contributed to the understanding of genetic diversity, the mechanisms involved in drug resistance and the transmission dynamics of this pathogen. The object of this study is to use WGS for the epidemiological and molecular characterization of M. tuberculosis clinical strains from Chinchiná, Caldas, a small town in Colombia with a high incidence of TB. Sputum samples were obtained during the first semester of 2020 from six patients and cultured in solid Löwenstein-Jensen medium. DNA extraction was obtained from positive culture samples and WGS was performed with the Illumina HiSeq 2500 platform for subsequent bioinformatic analysis. M. tuberculosis isolates were typified as Euro-American lineage 4 with a predominance of the Harlem and LAM sublineages. All samples were proven sensitive to antituberculosis drugs by genomic analysis, although no phenotype antimicrobial tests were performed on the samples, unreported mutations were identified that could require further analysis. The present study provides preliminary data for the construction of a genomic database line and the follow-up of lineages in this region.
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Affiliation(s)
- Lusayda Sánchez-Corrales
- Maestría en Investigación en Enfermedades Infecciosas, Universidad de Santander, Bucaramanga, Santander, Colombia
| | | | - Narmer Fernando Galeano-Vanegas
- Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Manizales, Caldas, Colombia
- Departamento de Biotecnología, BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
| | | | | | | | - Johan Sebastián Hernández-Botero
- Grupo de Investigación Médica, Escuela de Medicina, Universidad de Manizales, Manizales, Caldas, Colombia
- Grupo de Resistencia Antibiótica de Manizales, Manizales, Caldas, Colombia
| | - Fernando Siller-López
- Programa de Bacteriología, Universidad Católica de Manizales, Manizales, Caldas, Colombia
- Programa de Microbiología, Universidad Libre, Pereira, Risaralda, Colombia
- * E-mail:
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15
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Bogaerts B, Delcourt T, Soetaert K, Boarbi S, Ceyssens PJ, Winand R, Van Braekel J, De Keersmaecker SCJ, Roosens NHC, Marchal K, Mathys V, Vanneste K. A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. J Clin Microbiol 2021; 59:e00202-21. [PMID: 33789960 PMCID: PMC8316078 DOI: 10.1128/jcm.00202-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/27/2021] [Indexed: 01/18/2023] Open
Abstract
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.
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Affiliation(s)
- Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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16
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GenSeizer: a Multiplex PCR-Based Targeted Gene Sequencing Platform for Rapid and Accurate Identification of Major Mycobacterium Species. J Clin Microbiol 2021; 59:JCM.00584-20. [PMID: 33177124 PMCID: PMC8111139 DOI: 10.1128/jcm.00584-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis and nontuberculous mycobacterium (NTM) infections often exhibit similar clinical symptoms. Timely and effective treatment relies on the rapid and accurate identification of species and resistance genotypes. In this study, a new platform (GenSeizer), which combines bioinformatics analysis of a large data set and multiplex PCR-based targeted gene sequencing, was developed to identify 10 major Mycobacterium species that cause pulmonary, as well as extrapulmonary, human diseases. The simultaneous detection of certain erm(41) and rrl resistance genotypes in M. abscessus was also feasible. This platform was specific and sensitive and exhibited no cross-reactivity among reference strains and a detection limit of 5 DNA copies or 50 CFU Mycobacterium/ml. In a blind comparison, GenSeizer and multigene sequencing showed 100% agreement in the ability to identify 88 clinical Mycobacterium isolates. The resistance genotypes, confirmed by whole-genome sequencing of 30 M. abscessus strains, were also correctly identified by GenSeizer 100% of the time. These results indicate that GenSeizer is an efficient, reliable platform for detecting major pathogenic Mycobacterium species.
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17
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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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18
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Adewumi AT, Elrashedy A, Soremekun OS, Ajadi MB, Soliman MES. Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124. J Biomol Struct Dyn 2020; 40:2934-2954. [PMID: 33155529 DOI: 10.1080/07391102.2020.1844061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb) encoded secreted antigen 85 enzymes (Ag85A/Ag85B/Ag85C) play that critical roles in the virulence, survival and drug-resistant TB of the pathogen. Ag85 proteins are potential antitubercular drug targets because they are essential in the catalytic synthesis of trehalose moieties and mycolic acid attachment to the Mtb cell wall. Recently, experimental protocols led to the discovery of a selective covalent Ag85 inhibitor, β-isomer monocyclic enolphosphorus Cycliphostin (CyC8β) compound, which targets the Ag85 serine 124 to exhibit a promising therapeutic activity. For the first time, our study unravelled the structural features among Mtb Ag85C homologs and motions and dynamics of Ag85C when the CyC8β bound covalently and in open model conformations to the protein using bioinformatics tools and integrated Molecular dynamics simulations. Comparative Ag85C sequence analysis revealed conserved regions; 70% active site, 90% Adeniyi loop L1 and 50% loop L2, which acts as a switch between open and closed conformations. The average C-α atoms RMSD (2.05 Å) and RMSF (0.9 Å) revealed instability and high induced flexibility in the CyC8β covalent-bound compared to the apo and open model systems, which displayed more stability and lower fluctuations. DSSP showed structural transitions of α-helices to bend and loops to 310-helices in the bound systems. SASA of CyC8β covalent bound showed active site hydrophobic residues exposure to huge solvent. Therefore, these findings present the potential opportunity hotspots in Ag85C protein that would aid the structure-based design of novel chemical entities capable of resulting in potent antitubercular drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeniyi T Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed Elrashedy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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19
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Singh P, Amir M, Chaudhary U, Ahmad F, Bhatt S, Sankhwar S, Dohare R. Identification of robust genes in transcriptional regulatory network of Mycobacterium tuberculosis. IET Syst Biol 2020; 14:292-296. [PMID: 33095750 PMCID: PMC8687171 DOI: 10.1049/iet-syb.2020.0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/11/2020] [Accepted: 07/24/2020] [Indexed: 01/21/2023] Open
Abstract
About 30% of the world population is infected with Mycobacterium tuberculosis (MTB). It is well known that the gene expression in MTB is highly variable, thus screening of traditional single-gene in MTB has been incapable to meet the desires of clinical diagnosis. In this report, the authors systemically analysed the transcription regulatory network (TRN) in MTB H37Rv. The complex interplay of these gene interactions has been revealed using exhaustive topological and global analysis of TRN using parameters including indegree, outdegree, degree, directed and undirected average path length (APL), and randomly performed. Results from indegree analysis reveal a set of important genes, including papA5 and Rv0177 which are associated with high indegree values. Gene ontology analysis suggested their importance in the virulence of MTB. In addition, APL and analysis of highly significant genes further identified some critical genes with different APL values. Among the list of genes identified, the csoR gene has the shortest directed APL score and high outdegree value, thus suggesting their importance in maintaining network topology. This study provides a comprehensive analysis of TRN and offers a good basis of understanding for developing experimental study in search of new therapeutic targets against MTB H37Rv pathogen.
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Affiliation(s)
- Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Upasana Chaudhary
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Fozail Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Sachin Bhatt
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shweta Sankhwar
- Department of Information Technology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020; 21:ijms21196979. [PMID: 32977381 PMCID: PMC7582311 DOI: 10.3390/ijms21196979] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the “omics” approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.
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Mutations in Mycobacterium tuberculosis Isolates with Discordant Results for Drug-Susceptibility Testing in Peru. Int J Microbiol 2020; 2020:8253546. [PMID: 32322275 PMCID: PMC7166257 DOI: 10.1155/2020/8253546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/18/2020] [Indexed: 11/27/2022] Open
Abstract
Evaluation of resistance to antituberculosis drugs is routinely performed with genotypic or phenotypic methods; however, discordance can be seen between these different methodologies. Our objective was to identify mutations that could explain discordant results in the evaluation of susceptibility to rifampicin and isoniazid between molecular and phenotypic methods, using whole genome sequencing (WGS). Peruvian strains showing sensitive results in the GenoType MTBDRplus v2.0 test and resistant results in the proportions in the agar-plaque test for isoniazid or rifampin were selected. Discordance was confirmed by repeating both tests, and WGS was performed, using the Next Generation Sequencing methodology. Obtained sequences were aligned “through reference” (genomic mapping) using the program BWA with the algorithm “mem”, using as a reference the genome of the M. tuberculosis H37Rv strain. Discordance was confirmed in 14 strains for rifampicin and 21 for isoniazid, with 1 strain in common for both antibiotics, for a total of 34 unique strains. The most frequent mutation in the rpoB gene in the discordant strains for rifampicin was V170F. The most frequent mutations in the discordant strains for isoniazid were katG R463L, kasA G269S, and Rv1592c I322V. Several other mutations are reported. This is the first study in Latin America addressing mutations present in strains with discordant results between genotypic and phenotypic methods to rifampicin and isoniazid. These mutations could be considered as future potential targets for genotypic tests for evaluation of susceptibility to these drugs.
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Spitaleri A, Ghodousi A, Miotto P, Cirillo DM. Whole genome sequencing in Mycobacterium tuberculosis. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S197. [PMID: 31656776 DOI: 10.21037/atm.2019.07.28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Arnedo-Pena A, Romeu-Garcia MA, Meseguer-Ferrer N, Vivas-Fornas I, Vizcaino-Batllés A, Safont-Adsuara L, Bellido-Blasco JB, Moreno-Muñoz R. Pulmonary Versus Extrapulmonary Tuberculosis Associated Factors: A Case-Case Study. Microbiol Insights 2019; 12:1178636119840362. [PMID: 30992667 PMCID: PMC6449815 DOI: 10.1177/1178636119840362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) incidence remains low in health departments of Castellon and La Plana-Vila-real, but TB elimination is challenging. The objective of this study was to estimate associated factors of pulmonary tuberculosis (PTB) compared with extrapulmonary tuberculosis (ETB) and investigate epidemiological characteristics of these pathologies to orient control and prevention actions. MATERIALS AND METHODS A prospective case-case study was implemented by comparing PTB and ETB incidences during 2013-2016 from notification reports, epidemiological surveillance, and microbiological results of hospitals' laboratories Hospital General Castellon and La Plana-Vila-Real in the province of Castellon of Valencia region in Spain. In this design, cases were patients with PTB and controls were patients with ETB. Directed acyclic graph approach was used for selection of potential risk and confounding factors. Adjusted odds ratios (AORs) were estimated by logistic regression models. RESULTS The study included 136 patients with PTB and 57 patients with ETB, with microbiological confirmation of 93.4% and 52.6%, and the annual median of incidence rates were 7.5 and 3.1 per 100 000 inhabitants, respectively. In general, patients with PTB were younger with higher male proportion than patients with ETB. Risk factors of PTB were smoking tobacco (AOR = 3.98; 95% confidence interval [CI] = 1.66-9.56), social problems (social marginalization, homeless, residence in shelters for the poor, or stay in prison) (AOR = 3.39; 95% CI = 1.05-10.94), and contact with patients with TB (AOR = 2.51; 95% CI = 1.06-5.95). No-smoking tobacco and no-drug abuse interaction decrease PTB risk (AOR = 0.27; 95% CI = 0.12-0.64). From these results, specific measures of health promotion and prevention can be addressed. CONCLUSIONS The estimated associated factors of PTB may be prevented, and it was demonstrated that the case-case design is useful in the study of TB.
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Affiliation(s)
- Alberto Arnedo-Pena
- Epidemiology Division, Public Health
Center, Castellon, Spain
- Department Medicine Preventive and
Public Health, Faculty of Health Sciences, Public University of Navarra, Pamplona,
Spain
- CIBER—Epidemiology and Public Health,
Barcelona, Spain
| | | | | | | | | | | | - Juan Bautista Bellido-Blasco
- Epidemiology Division, Public Health
Center, Castellon, Spain
- CIBER—Epidemiology and Public Health,
Barcelona, Spain
- Department of Epidemiology and Public
Health. School of Medicine, Jaume I University, Castellon, Spain
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