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  1. Article ; Online: Phenogenomics of Mycobacterium abscessus.

    Comas, Iñaki / Moreno-Molina, Miguel

    Nature microbiology

    2022  Volume 7, Issue 9, Page(s) 1325–1326

    MeSH term(s) Mycobacterium abscessus
    Language English
    Publishing date 2022-08-25
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-022-01217-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Genomic Epidemiology of Tuberculosis.

    Comas, Iñaki

    Advances in experimental medicine and biology

    2017  Volume 1019, Page(s) 79–93

    Abstract: The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical ... ...

    Abstract The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still exploring the wider potential of this new technology. Whole genome sequencing in tuberculosis still requires bacterial cultures. Thus, although whole genome sequencing has revolutionized the interpretation of transmission patterns, it is not yet ready to be applied at the point-of-care. In this chapter, I will review the promises and challenges of genomic epidemiology, as well as some of the new questions that have arisen from the use of this new technology. In addition, I will examine the role of molecular epidemiology within the general frame of global tuberculosis control and how genomic epidemiology can contribute towards the elimination of the disease.
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-319-64371-7_4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Legionella effectors reflect strength in diversity.

    Comas, Iñaki

    Nature genetics

    2016  Volume 48, Issue 2, Page(s) 115–116

    Abstract: The Legionella genus includes opportunistic human pathogenic species that invade human cells using effector proteins that evolved during association with their natural amoeba hosts. A new study compares the genomes of 41 Legionella species to identify ... ...

    Abstract The Legionella genus includes opportunistic human pathogenic species that invade human cells using effector proteins that evolved during association with their natural amoeba hosts. A new study compares the genomes of 41 Legionella species to identify nearly 6,000 effectors, providing insight into these species' evolution and pathogenic lifestyles.
    MeSH term(s) Genome, Bacterial ; Legionella/genetics
    Language English
    Publishing date 2016-02
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.3492
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  4. Article ; Online: Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex.

    Chiner-Oms, Álvaro / Comas, Iñaki

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2019  Volume 72, Page(s) 10–15

    Abstract: Two strains of Mycobacterium tuberculosis complex can be separated as much as 2500 single nucleotide differences (Coscolla and Gagneux, 2014). In that limited amount of diversity, we find an astonishing range of clinical, epidemiological and biological ... ...

    Abstract Two strains of Mycobacterium tuberculosis complex can be separated as much as 2500 single nucleotide differences (Coscolla and Gagneux, 2014). In that limited amount of diversity, we find an astonishing range of clinical, epidemiological and biological phenotypes. The most striking is the strong host preferences depending on the infecting strain while more subtle differences can be found looking at different human tuberculosis isolates. Those subtle differences are the most difficult to spot given that analysis methods for so little diversity are limited and phenotypes like virulence are difficult to define and measure. Recent genomics advances allow to study the pathogen diversity at a resolution not available before from comparative species level, to global diversity to transmission in local settings. Here, we will review some of these recent results to highlight how population genomics approaches can aid not only to understand how MTBC evolved but also to identify relevant biomedical targets.
    MeSH term(s) Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/genetics ; Genomics ; Host-Pathogen Interactions/genetics ; Humans ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Tuberculosis ; Virulence Factors/genetics
    Chemical Substances Virulence Factors
    Language English
    Publishing date 2019-02-26
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2019.02.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5645: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Epidemiological cluster identification using multiple data sources: an approach using logistic regression.

    Susvitasari, Kurnia / Tupper, Paul F / Cancino-Muños, Irving / Lòpez, Mariana G / Comas, Iñaki / Colijn, Caroline

    Microbial genomics

    2023  Volume 9, Issue 3

    Abstract: In the management of infectious disease outbreaks, grouping cases into clusters and understanding their underlying epidemiology are fundamental tasks. In genomic epidemiology, clusters are typically identified either using pathogen sequences alone or ... ...

    Abstract In the management of infectious disease outbreaks, grouping cases into clusters and understanding their underlying epidemiology are fundamental tasks. In genomic epidemiology, clusters are typically identified either using pathogen sequences alone or with sequences in combination with epidemiological data such as location and time of collection. However, it may not be feasible to culture and sequence all pathogen isolates, so sequence data may not be available for all cases. This presents challenges for identifying clusters and understanding epidemiology, because these cases may be important for transmission. Demographic, clinical and location data are likely to be available for unsequenced cases, and comprise partial information about their clustering. Here, we use statistical modelling to assign unsequenced cases to clusters already identified by genomic methods, assuming that a more direct method of linking individuals, such as contact tracing, is not available. We build our model on pairwise similarity between cases to predict whether cases cluster together, in contrast to using individual case data to predict the cases' clusters. We then develop methods that allow us to determine whether a pair of unsequenced cases are likely to cluster together, to group them into their most probable clusters, to identify which are most likely to be members of a specific (known) cluster, and to estimate the true size of a known cluster given a set of unsequenced cases. We apply our method to tuberculosis data from Valencia, Spain. Among other applications, we find that clustering can be predicted successfully using spatial distance between cases and whether nationality is the same. We can identify the correct cluster for an unsequenced case, among 38 possible clusters, with an accuracy of approximately 35 %, higher than both direct multinomial regression (17 %) and random selection (< 5 %).
    MeSH term(s) Humans ; Cluster Analysis ; Disease Outbreaks ; Genomics ; Logistic Models
    Language English
    Publishing date 2023-02-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000929
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: TB Transmission: Closing the Gaps.

    Comas, Iñaki / Gardy, Jennifer L

    EBioMedicine

    2018  Volume 34, Page(s) 4–5

    MeSH term(s) Education, Medical, Continuing ; Humans ; Mycobacterium tuberculosis/genetics ; Tuberculosis/diagnosis ; Tuberculosis/epidemiology ; Tuberculosis/genetics ; Tuberculosis/transmission
    Language English
    Publishing date 2018-07-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2018.07.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7090: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  7. Book ; Online: Iñaki Comas, investigador

    Comas, Iñaki / Estévez Torreblanca, Marina

    La nueva variante de COVID demuestra que hay que saber tomar a tiempo medidas para evitar una propagación tan rápida

    2020  

    Abstract: El investigador del Consejo Superior de Investigaciones Científicas (CSIC) en el Instituto de Biomedicina de Valencia (IBV-CSIC) y director del consorcio SeqCovid–España, Iñaki Comas, dejó de lado sus investigaciones sobre tuberculosis para dedicarse de ... ...

    Abstract El investigador del Consejo Superior de Investigaciones Científicas (CSIC) en el Instituto de Biomedicina de Valencia (IBV-CSIC) y director del consorcio SeqCovid–España, Iñaki Comas, dejó de lado sus investigaciones sobre tuberculosis para dedicarse de lleno al estudio y secuenciación del SARS-CoV-2, causante de la COVID. Les llega información a través de las muestras PCR que toman los laboratorios para poder conocer el rastro genético del virus, a lo que se añaden las secuenciaciones que hacen algunos hospitales. España es el segundo país de Europa y el cuarto del mundo que más secuencias genéticas obtiene de este virus. "Eso nos permite ver cosas que otros países no pueden ver", explica Comas, coautor de un estudio liderado por Suiza que está intentado determinar los caminos que siguen las distintas cepas y variantes del virus causante de esta pandemia.

    No
    Keywords covid19
    Language Spanish
    Publishing date 2020-10-29
    Publisher Diario de Prensa Digital
    Publishing country es
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: ¿Cuál es la forma de transmisión del virus? ; Novedades en transmisión

    Comas, Iñaki / Querol, Xavier

    2020  

    Abstract: El informe está disponible en DIGITAL.CSIC: Una visión global de la pandemia COVID-19: qué sabemos y qué estamos investigando desde el CSIC, http://dx.doi.org/10.20350/digitalCSIC/12596. Victoria Moreno, Vicepresidencia Adjunta de Áreas Científico- ... ...

    Abstract El informe está disponible en DIGITAL.CSIC: Una visión global de la pandemia COVID-19: qué sabemos y qué estamos investigando desde el CSIC, http://dx.doi.org/10.20350/digitalCSIC/12596. Victoria Moreno, Vicepresidencia Adjunta de Áreas Científico-Técnicas, coordinadora del informe.

    Consulta la web pública de la PTI Salud Global para conocer más noticias y novedades de la actividad de nuestros investigadores en la lucha contra la pandemia provocada por la COVID-19. Y si tienes cualquier consulta , puedes hacérnosla llegar a través del email: pti@csic.es

    DISPONIBLE PRÓXIMAMENTE

    Newsletter PTI Salud Global/Global Health Cov19: en esta sección se destacan las novedades mediante las que se actualiza el informe en el que los científicos del CSIC analizan los aspectos clave de la COVID-19 .

    Peer reviewed
    Keywords covid19
    Language Spanish
    Publishing date 2020-10-19
    Publisher Consejo Superior de Investigaciones Científicas (España)
    Publishing country es
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  9. Article ; Online: Gene evolutionary trajectories in

    Chiner-Oms, Álvaro / López, Mariana G / Moreno-Molina, Miguel / Furió, Victoria / Comas, Iñaki

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 17, Page(s) e2113600119

    Abstract: Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug resistance profiles. Said differences usually emerge ... ...

    Abstract Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug resistance profiles. Said differences usually emerge through de novo mutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ∼5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host–pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.
    MeSH term(s) Evolution, Molecular ; Genome, Bacterial ; Mutation ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA
    Language English
    Publishing date 2022-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2113600119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Show issues Location:
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  10. Article: Signatures of transmission in within-host

    Walter, Katharine S / Cohen, Ted / Mathema, Barun / Colijn, Caroline / Sobkowiak, Benjamin / Comas, Iñaki / Goig, Galo A / Croda, Julio / Andrews, Jason R

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Background: Because : Methods: To evaluate the transmission information present in within-host : Findings: We found moderate levels of minority variation present in : Interpretation: Within-host : Funding: NIAID: 5K01AI173385. ...

    Abstract Background: Because
    Methods: To evaluate the transmission information present in within-host
    Findings: We found moderate levels of minority variation present in
    Interpretation: Within-host
    Funding: NIAID: 5K01AI173385.
    Language English
    Publishing date 2023-12-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.12.28.23300451
    Database MEDical Literature Analysis and Retrieval System OnLINE

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