Publicação
A genomic exploration of transmissibility in Mycobacterium tuberculosis
| Resumo: | The ability of Mycobacterium tuberculosis (Mtb) to be transmitted from host to host is not well understood. Previous molecular epidemiology studies have shown that while some clinical strains of Mtb are able to cause infection and disease in a large number of individuals exposed to them, others are confined in their transmission, despite the ample chance for the spread of the infection. Since preventing transmission of Mtb is the key to a continued decline in tuberculosis cases, understanding the host and bacterial factors that are associated with transmissibility could be useful in developing strategies to prevent transmission. Previous work has focused on cluster size as a measurable proxy for transmissibility, and several studies have found that host risk factors are associated with clustering and cluster size. This thesis set out to explore if and what bacterial factors, such as phylogenetic lineage and genomic markers, lie behind an increased transmissibility phenotype. We describe a novel approach, called the Propensity to Propagate (PPP), with which to adjust for host risk factors when quantifying transmissibility. Using this method, we found no significant differences to propagate between four different lineages within the Netherlands, as measured by molecular-typing defined cluster sizes. When looking more specifically at infectivity (as defined by mean number of positive contacts around each patient) and number of secondary cases within two years after diagnosis of an index case sharing the same fingerprint, we found evidence of phylogenetic lineage influencing these two indicators, namely, a decreased ability to infect and a lower secondary case rate in ancient phylogenetic lineages (Mycobacterium africanum and EAI) compared to their modern counterparts (Euro-American, Beijing, and CAS). One simple approach to discovering more specific genetic regions behind transmissibility involves checking the absence/presence of mutations in the genes of interest between transmissible and nontransmissible phenotypes. In one of our studies, a multivariate logistic regression-based analysis of patient-, microorganism- and disease-related factors failed to reveal any significant association between frameshift-causing indels in Mycobacterium cyclase/LuxR-like genes (mclxs) and transmissibility. Finally, using a large, well-characterized, complete data set of typed strains to identify strains found in large clusters as a proxy for a transmission phenotype as well as related strains that have not been transmitted, we selected 100 bacterial isolates after controlling for epidemiologic and host factors that may influence transmission. After whole genome sequencing, we subjected them to evolutionary convergence analysis. We identified six bacterial DNA regions - espE, PE-PGRS33, PE-PGRS56, Rv0197, Rv2813-14c and Rv2815-16c - to be associated with Mtb transmission and validated these regions by studying the response of human white blood cells to extracts from a subset of the tuberculosis bacteria that carried or did not carry mutations in these DNA regions. We show that there are differences in the immune response – as reflected by in vitro monocyte and T-cell cytokine production, reactive oxygen species release and neutrophil apoptosis - that associate with these genetic changes. These findings not only contribute to our understanding of the interplay of bacterial factors in creating more successful strains at transmitting, but also have implications in the future of disease surveillance and curbing of transmission, by providing for instance tools with which to flag patients carrying particularly transmissible strains. |
|---|---|
| Autores principais: | Guimarães, Hanna Nebenzahl |
| Assunto: | Ciências Médicas::Ciências da Saúde |
| Ano: | 2016 |
| País: | Portugal |
| Tipo de documento: | tese de doutoramento |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| _version_ | 1867438358436773888 |
|---|---|
| author | Guimarães, Hanna Nebenzahl |
| author_facet | Guimarães, Hanna Nebenzahl |
| author_role | author |
| contributor_name_str_mv | Neves, Margarida Correia Murray, Megan B. RepositóriUM - Universidade do Minho |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Guimarães, Hanna Nebenzahl\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Neves, Margarida Correia Murray, Megan B. RepositóriUM - Universidade do Minho |
| datacite.creators.creator.creatorName.fl_str_mv | Guimarães, Hanna Nebenzahl |
| datacite.date.Accepted.fl_str_mv | 2016-07-25T00:00:00Z |
| datacite.date.available.fl_str_mv | 2016-12-02T16:07:04Z |
| datacite.date.embargoed.fl_str_mv | 2016-12-02T16:07:04Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Ciências Médicas::Ciências da Saúde |
| datacite.titles.title.fl_str_mv | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| dc.contributor.none.fl_str_mv | Neves, Margarida Correia Murray, Megan B. RepositóriUM - Universidade do Minho |
| dc.creator.none.fl_str_mv | Guimarães, Hanna Nebenzahl |
| dc.date.Accepted.fl_str_mv | 2016-07-25T00:00:00Z |
| dc.date.available.fl_str_mv | 2016-12-02T16:07:04Z |
| dc.date.embargoed.fl_str_mv | 2016-12-02T16:07:04Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | https://hdl.handle.net/1822/43236 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | Ciências Médicas::Ciências da Saúde |
| dc.title.fl_str_mv | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_db06 |
| description | The ability of Mycobacterium tuberculosis (Mtb) to be transmitted from host to host is not well understood. Previous molecular epidemiology studies have shown that while some clinical strains of Mtb are able to cause infection and disease in a large number of individuals exposed to them, others are confined in their transmission, despite the ample chance for the spread of the infection. Since preventing transmission of Mtb is the key to a continued decline in tuberculosis cases, understanding the host and bacterial factors that are associated with transmissibility could be useful in developing strategies to prevent transmission. Previous work has focused on cluster size as a measurable proxy for transmissibility, and several studies have found that host risk factors are associated with clustering and cluster size. This thesis set out to explore if and what bacterial factors, such as phylogenetic lineage and genomic markers, lie behind an increased transmissibility phenotype. We describe a novel approach, called the Propensity to Propagate (PPP), with which to adjust for host risk factors when quantifying transmissibility. Using this method, we found no significant differences to propagate between four different lineages within the Netherlands, as measured by molecular-typing defined cluster sizes. When looking more specifically at infectivity (as defined by mean number of positive contacts around each patient) and number of secondary cases within two years after diagnosis of an index case sharing the same fingerprint, we found evidence of phylogenetic lineage influencing these two indicators, namely, a decreased ability to infect and a lower secondary case rate in ancient phylogenetic lineages (Mycobacterium africanum and EAI) compared to their modern counterparts (Euro-American, Beijing, and CAS). One simple approach to discovering more specific genetic regions behind transmissibility involves checking the absence/presence of mutations in the genes of interest between transmissible and nontransmissible phenotypes. In one of our studies, a multivariate logistic regression-based analysis of patient-, microorganism- and disease-related factors failed to reveal any significant association between frameshift-causing indels in Mycobacterium cyclase/LuxR-like genes (mclxs) and transmissibility. Finally, using a large, well-characterized, complete data set of typed strains to identify strains found in large clusters as a proxy for a transmission phenotype as well as related strains that have not been transmitted, we selected 100 bacterial isolates after controlling for epidemiologic and host factors that may influence transmission. After whole genome sequencing, we subjected them to evolutionary convergence analysis. We identified six bacterial DNA regions - espE, PE-PGRS33, PE-PGRS56, Rv0197, Rv2813-14c and Rv2815-16c - to be associated with Mtb transmission and validated these regions by studying the response of human white blood cells to extracts from a subset of the tuberculosis bacteria that carried or did not carry mutations in these DNA regions. We show that there are differences in the immune response – as reflected by in vitro monocyte and T-cell cytokine production, reactive oxygen species release and neutrophil apoptosis - that associate with these genetic changes. These findings not only contribute to our understanding of the interplay of bacterial factors in creating more successful strains at transmitting, but also have implications in the future of disease surveillance and curbing of transmission, by providing for instance tools with which to flag patients carrying particularly transmissible strains. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | doctoralThesis |
| fulltext.url.fl_str_mv | https://repositorium.uminho.pt/bitstreams/1c74fa89-f6ba-4a96-8fb0-1512333d7cb6/download |
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| identifier.url.fl_str_mv | https://hdl.handle.net/1822/43236 |
| instacron_str | repositorium |
| institution | Universidade do Minho |
| instname_str | Universidade do Minho |
| language | eng |
| network_acronym_str | rum |
| network_name_str | RepositóriUM - Universidade do Minho |
| oai_identifier_str | oai:repositorium.uminho.pt:1822/43236 |
| organization_str_mv | urn:organizationAcronym:repositorium |
| person_str_mv | Guimarães, Hanna Nebenzahl |
| publishDate | 2016 |
| reponame_str | RepositóriUM - Universidade do Minho |
| repository_id_str | urn:repositoryAcronym:rum |
| service_str_mv | urn:repositoryAcronym:rum |
| spelling | engporThe ability of Mycobacterium tuberculosis (Mtb) to be transmitted from host to host is not well understood. Previous molecular epidemiology studies have shown that while some clinical strains of Mtb are able to cause infection and disease in a large number of individuals exposed to them, others are confined in their transmission, despite the ample chance for the spread of the infection. Since preventing transmission of Mtb is the key to a continued decline in tuberculosis cases, understanding the host and bacterial factors that are associated with transmissibility could be useful in developing strategies to prevent transmission. Previous work has focused on cluster size as a measurable proxy for transmissibility, and several studies have found that host risk factors are associated with clustering and cluster size. This thesis set out to explore if and what bacterial factors, such as phylogenetic lineage and genomic markers, lie behind an increased transmissibility phenotype. We describe a novel approach, called the Propensity to Propagate (PPP), with which to adjust for host risk factors when quantifying transmissibility. Using this method, we found no significant differences to propagate between four different lineages within the Netherlands, as measured by molecular-typing defined cluster sizes. When looking more specifically at infectivity (as defined by mean number of positive contacts around each patient) and number of secondary cases within two years after diagnosis of an index case sharing the same fingerprint, we found evidence of phylogenetic lineage influencing these two indicators, namely, a decreased ability to infect and a lower secondary case rate in ancient phylogenetic lineages (Mycobacterium africanum and EAI) compared to their modern counterparts (Euro-American, Beijing, and CAS). One simple approach to discovering more specific genetic regions behind transmissibility involves checking the absence/presence of mutations in the genes of interest between transmissible and nontransmissible phenotypes. In one of our studies, a multivariate logistic regression-based analysis of patient-, microorganism- and disease-related factors failed to reveal any significant association between frameshift-causing indels in Mycobacterium cyclase/LuxR-like genes (mclxs) and transmissibility. Finally, using a large, well-characterized, complete data set of typed strains to identify strains found in large clusters as a proxy for a transmission phenotype as well as related strains that have not been transmitted, we selected 100 bacterial isolates after controlling for epidemiologic and host factors that may influence transmission. After whole genome sequencing, we subjected them to evolutionary convergence analysis. We identified six bacterial DNA regions - espE, PE-PGRS33, PE-PGRS56, Rv0197, Rv2813-14c and Rv2815-16c - to be associated with Mtb transmission and validated these regions by studying the response of human white blood cells to extracts from a subset of the tuberculosis bacteria that carried or did not carry mutations in these DNA regions. We show that there are differences in the immune response – as reflected by in vitro monocyte and T-cell cytokine production, reactive oxygen species release and neutrophil apoptosis - that associate with these genetic changes. These findings not only contribute to our understanding of the interplay of bacterial factors in creating more successful strains at transmitting, but also have implications in the future of disease surveillance and curbing of transmission, by providing for instance tools with which to flag patients carrying particularly transmissible strains.application/pdfporA genomic exploration of transmissibility in Mycobacterium tuberculosisGuimarães, Hanna NebenzahlNeves, Margarida CorreiaMurray, Megan B.HostingInstitutionOrganizationalRepositóriUM - Universidade do Minhoe-mailmailto:repositorium@usdb.uminho.ptrepositorium@usdb.uminho.ptTID1015138522016-12-02T16:07:04Z2016-07-252016-04-252016-07-25T00:00:00ZHandlehttps://hdl.handle.net/1822/43236http://purl.org/coar/access_right/c_abf2open accesshttp://www.oecd.org/science/inno/38235147.pdfFields of Science and Technology (FOS)Ciências Médicas::Ciências da Saúde8842039 bytesliteraturehttp://purl.org/coar/resource_type/c_db06doctoral thesishttp://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://repositorium.uminho.pt/bitstreams/1c74fa89-f6ba-4a96-8fb0-1512333d7cb6/download |
| spellingShingle | A genomic exploration of transmissibility in Mycobacterium tuberculosis Guimarães, Hanna Nebenzahl Ciências Médicas::Ciências da Saúde |
| status | SINGLETON |
| subject.other.fl_str_mv | Ciências Médicas::Ciências da Saúde |
| title | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| title_full | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| title_fullStr | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| title_full_unstemmed | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| title_short | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| title_sort | A genomic exploration of transmissibility in Mycobacterium tuberculosis |
| topic | Ciências Médicas::Ciências da Saúde |
| topic_facet | Ciências Médicas::Ciências da Saúde |
| url | https://hdl.handle.net/1822/43236 |
| visible | 1 |