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García-Marín AM, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, González-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, González-Candelas F, Furió V, Comas I. Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis. Lancet Microbe 2024; 5:e43-e51. [PMID: 38061383 PMCID: PMC10790317 DOI: 10.1016/s2666-5247(23)00252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. METHODS In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. FINDINGS WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. INTERPRETATION We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. FUNDING European Research Council and the Spanish Ministerio de Ciencia.
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Affiliation(s)
- Ana María García-Marín
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain
| | - Irving Cancino-Muñoz
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain
| | | | | | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J Camarena
- Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Ester Colomer-Roig
- FISABIO Public Health, Valencia, Spain; Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lirios, Alcoy, Spain
| | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicante, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital Francesc de Borja, Gandía, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia, Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Hermelinda Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia, Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-University of Valencia, Institute for Integrative Systems Biology, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Victoria Furió
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain.
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Valencia, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
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Cancino-Muñoz I, López MG, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colijn C, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, García-García F, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, Gónzales-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, Comas I. Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics. eLife 2022; 11:76605. [PMID: 35880398 PMCID: PMC9323001 DOI: 10.7554/elife.76605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Transmission is a driver of tuberculosis (TB) epidemics in high-burden regions, with assumed negligible impact in low-burden areas. However, we still lack a full characterization of transmission dynamics in settings with similar and different burdens. Genomic epidemiology can greatly help to quantify transmission, but the lack of whole genome sequencing population-based studies has hampered its application. Here, we generate a population-based dataset from Valencia region and compare it with available datasets from different TB-burden settings to reveal transmission dynamics heterogeneity and its public health implications. We sequenced the whole genome of 785 Mycobacterium tuberculosis strains and linked genomes to patient epidemiological data. We use a pairwise distance clustering approach and phylodynamic methods to characterize transmission events over the last 150 years, in different TB-burden regions. Our results underscore significant differences in transmission between low-burden TB settings, i.e., clustering in Valencia region is higher (47.4%) than in Oxfordshire (27%), and similar to a high-burden area as Malawi (49.8%). By modeling times of the transmission links, we observed that settings with high transmission rate are associated with decades of uninterrupted transmission, irrespective of burden. Together, our results reveal that burden and transmission are not necessarily linked due to the role of past epidemics in the ongoing TB incidence, and highlight the need for in-depth characterization of transmission dynamics and specifically tailored TB control strategies.
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Affiliation(s)
- Irving Cancino-Muñoz
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Mariana G López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Luis M Villamayor
- Unidad Mixta "Infección y Salud Pública" (FISABIO-CSISP), Valencia, Spain
| | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J Camarena
- Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Caroline Colijn
- Department of Mathematics, Faculty of Science, Simon Fraser University, Burnaby, Canada
| | - Ester Colomer-Roig
- Unidad Mixta "Infección y Salud Pública" (FISABIO-CSISP), Valencia, Spain.,Microbiology Service, Hospital Universitario Dr Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lirios, Alcoy, Spain
| | | | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicantes, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellón, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicantes, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia (DGSP), Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Hermelinda Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud y Sanidad Ambiental de Valencia (DGSP), Valencia, Spain
| | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
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3
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Furió V, Moreno-Molina M, Chiner-Oms Á, Villamayor LM, Torres-Puente M, Comas I. An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis. Commun Biol 2021; 4:1322. [PMID: 34819627 PMCID: PMC8613195 DOI: 10.1038/s42003-021-02846-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Efforts to eradicate tuberculosis are hampered by the rise and spread of antibiotic resistance. Several large-scale projects have aimed to specifically link clinical mutations to resistance phenotypes, but they were limited in both their explanatory and predictive powers. Here, we combine functional genomics and phylogenetic associations using clinical strain genomes to decipher the architecture of isoniazid resistance and search for new resistance determinants. This approach has allowed us to confirm the main target route of the antibiotic, determine the clinical relevance of redox metabolism as an isoniazid resistance mechanism and identify novel candidate genes harboring resistance mutations in strains with previously unexplained isoniazid resistance. This approach can be useful for characterizing how the tuberculosis bacilli acquire resistance to new antibiotics and how to forestall them. Victoria Furió et al. apply functional genomics and evolutionary analyses to the study of antibiotic resistance in tuberculosis. Focusing on isoniazid resistance and using genomic data from clinical strains, they identify novel candidate genes with resistance mutations and further uncover the mechanisms underlying drug resistance.
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Affiliation(s)
- Victoria Furió
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain.
| | | | - Álvaro Chiner-Oms
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain
| | | | | | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain.,CIBER in Epidemiology and Public Health, Madrid, 28029, Spain
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Goig GA, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Navarro D, Borrás R, Comas I. Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study. The Lancet Microbe 2020; 1:e175-e183. [DOI: 10.1016/s2666-5247(20)30060-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
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5
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Cancino-Muñoz I, Moreno-Molina M, Furió V, Goig GA, Torres-Puente M, Chiner-Oms Á, Villamayor LM, Sanz F, Guna-Serrano MR, Comas I. Cryptic Resistance Mutations Associated With Misdiagnoses of Multidrug-Resistant Tuberculosis. J Infect Dis 2020; 220:316-320. [PMID: 30875421 PMCID: PMC6581888 DOI: 10.1093/infdis/jiz104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
Understanding why some multidrug-resistant tuberculosis cases are not detected by rapid phenotypic and genotypic routine clinical tests is essential to improve diagnostic assays and advance toward personalized tuberculosis treatment. Here, we combine whole-genome sequencing with single-colony phenotyping to identify a multidrug-resistant strain that had infected a patient for 9 years. Our investigation revealed the failure of rapid testing and genome-based prediction tools to identify the multidrug-resistant strain. The false-negative findings were caused by uncommon rifampicin and isoniazid resistance mutations. Although whole-genome sequencing data helped to personalize treatment, the patient developed extensively drug-resistant tuberculosis, highlighting the importance of coupling new diagnostic methods with appropriate treatment regimens.
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Affiliation(s)
- Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas.,Genomics and Health Unit, FISABIO Public Health, Consorci Hospital General Universitari de València, Valencia, Spain
| | - Miguel Moreno-Molina
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Victoria Furió
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Galo A Goig
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Manuela Torres-Puente
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas
| | - Álvaro Chiner-Oms
- Unidad Mixta "Infección y Salud Pública," Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Conselleria de Sanitat Universal i Salut Pública
| | - Luis M Villamayor
- Genomics and Health Unit, FISABIO Public Health, Consorci Hospital General Universitari de València, Valencia, Spain
| | - Francisco Sanz
- Departamento de Neumología, Consorci Hospital General Universitari de València, Valencia, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
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6
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Goig GA, Torres-Puente M, Mariner-Llicer C, Villamayor LM, Chiner-Oms Á, Gil-Brusola A, Borrás R, Comas Espadas I. Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics. Bioinformatics 2020; 36:985-989. [PMID: 31580405 PMCID: PMC7703747 DOI: 10.1093/bioinformatics/btz729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/02/2019] [Accepted: 09/25/2019] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. RESULTS In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research. AVAILABILITY AND IMPLEMENTATION The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Galo A Goig
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Carla Mariner-Llicer
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Luis M Villamayor
- Genomics and Health Unit, FISABIO Public Health (CSISP), Valencia 46035, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
| | - Ana Gil-Brusola
- Microbiology Service, La Fe University and Polytechnic Hospital, Valencia 46026, Spain
| | - Rafael Borrás
- Microbiology Service, University Clinic Hospital, Valencia 46010, Spain
- Microbiology Department, School of Medicine, University of Valencia, Valencia 46010, Spain
| | - Iñaki Comas Espadas
- Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC), Valencia 46010, Spain
- CIBER in Epidemiology and Public Health, Madrid 28029, Spain
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7
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López MG, Dogba JB, Torres-Puente M, Goig GA, Moreno-Molina M, Villamayor LM, Cadmus S, Comas I. Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events. Microb Genom 2020; 6:e000325. [PMID: 31935183 PMCID: PMC7067037 DOI: 10.1099/mgen.0.000325] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) surveillance is scarce in most African countries, even though it is the continent with the greatest disease incidence according to the World Health Organization. Liberia is within the 30 countries with the highest TB burden, probably as a consequence of the long civil war and the recent Ebola outbreak, both crippling the health system and depreciating the TB prevention and control programmes. Due to difficulties working in the country, there is a lack of resistance surveys and bacillus characterization. Here, we use genome sequencing of Mycobacteriumtuberculosis clinical isolates to fill this gap. Our results highlight that the bacillus population structure is dominated by lineage 4 strains that harbour an outstanding genetic diversity, higher than in the rest of Africa as a whole. Coalescent analyses demonstrate that strains currently circulating in Liberia were introduced several times beginning in the early year 600 CE until very recently coinciding with migratory movements associated with the civil war and Ebola epidemics. A higher multidrug-resistant (MDR)-TB frequency (23.5 %) than current estimates was obtained together with non-catalogued drug-resistance mutations. Additionally, 39 % of strains were in genomic clusters revealing that ongoing transmission is a major contribution to the TB burden in the country. Our report emphasizes the importance of TB surveillance and control in African countries where bacillus diversity, MDR-TB prevalence and transmission are coalescing to jeopardize TB control programmes.
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Affiliation(s)
- Mariana G. López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - John B. Dogba
- Tuberculosis and Brucellosis Laboratories, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Nigeria
- Tuberculosis Laboratory, National Public Health Reference Laboratory, National Public Health Institute of Liberia, Margibi, Liberia
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Galo A. Goig
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Miguel Moreno-Molina
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Luis M. Villamayor
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- Unidad Mixta “Infección y Salud Pública” (FISABIO-CSISP), Valencia, Spain
| | - Simeon Cadmus
- Tuberculosis and Brucellosis Laboratories, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Nigeria
- Tuberculosis Laboratory, National Public Health Reference Laboratory, National Public Health Institute of Liberia, Margibi, Liberia
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
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8
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Xu Y, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrás R, Borrás-Máñez M, Bosque M, Camarena JJ, Colomer-Roig E, Colomina J, Escribano I, Esparcia-Rodríguez O, Gil-Brusola A, Gimeno C, Gimeno-Gascón A, Gomila-Sard B, González-Granda D, Gonzalo-Jiménez N, Guna-Serrano MR, López-Hontangas JL, Martín-González C, Moreno-Muñoz R, Navarro D, Navarro M, Orta N, Pérez E, Prat J, Rodríguez JC, Ruiz-García MM, Vanaclocha H, Colijn C, Comas I. High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS Med 2019; 16:e1002961. [PMID: 31671150 PMCID: PMC6822721 DOI: 10.1371/journal.pmed.1002961] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened. METHODS AND FINDINGS We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 [95% CI 0.02-1.10], p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region. CONCLUSIONS In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.
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Affiliation(s)
- Yuanwei Xu
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Rafael Borrás
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Borrás-Máñez
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | | | - Juan J. Camarena
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Ester Colomer-Roig
- Genomics and Health Unit, FISABIO Public Health, Valencia, Spain
- Microbiology Service, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Javier Colomina
- Microbiology and Parasitology Service, Hospital Universitario de La Ribera, Alzira, Spain
| | - Isabel Escribano
- Microbiology Laboratory, Hospital Virgen de los Lírios, Alcoy, Spain
| | | | - Ana Gil-Brusola
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Service, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - Bárbara Gomila-Sard
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | | | | | | | | | - Coral Martín-González
- Microbiology Service, Hospital Universitario de San Juan de Alicante, Alicante, Spain
| | - Rosario Moreno-Muñoz
- Microbiology Service, Hospital General Universitario de Castellón, Castellon, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Valencia, Spain
| | - María Navarro
- Microbiology Service, Hospital de la Vega Baixa, Orihuela, Spain
| | - Nieves Orta
- Microbiology Service, Hospital San Francesc de Borja, Gandía, Spain
| | - Elvira Pérez
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Josep Prat
- Microbiology Service, Hospital de Sagunto, Sagunto, Spain
| | | | | | - Herme Vanaclocha
- Subdirección General de Epidemiología y Vigilancia de la Salud, Dirección General de Salud Pública, Valencia, Spain
| | - Caroline Colijn
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (CC); (IC)
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
- * E-mail: (CC); (IC)
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