Ana C.
Reis
...
DP_AEM student
Centre for Ecology, Evolution and Environmental Changes
Doctoral Program in Biology (FCUL)
2016-2020
Mónica Cunha and Rogério Tenreiro
Ana
0
0

Phd Thesis

Systems epidemiology to devise new interventions for multi-host tuberculosis (PD/BD/128031/2016).
PhD in Biology, specialization at Microbiology. Doctoral thesis defended at 3rd November 2021 - Approved with honour and distinction (highest distinction)

Animal tuberculosis (TB) is an infectious disease of livestock and wildlife mainly caused by Mycobacterium bovis and, in a minor extent, Mycobacterium caprae.

In Portugal, animal TB is maintained in a multi-host system involving livestock and wild ungulates. The understanding of the processes driving transmission at this interface is key to inform control.

In this work, M. caprae isolates (n=55) from Portugal were characterized by spoligotyping and MIRU-VNTR, supporting the clonal structure, co-infection and in vivo microevolution of this ecotype.

M. bovis (n=948) from cattle, red deer and wild boar from TB hotspot regions were genotyped. Bayesian inference identified five ancestral populations and associated the most probable ancient M. bovis subpopulation with cattle and Beja, providing clues on the epidemics origin. A multinomial spatiotemporal probability model identified two significant TB clusters: one that persisted in 2004-2010 with Barrancos (Beja) at the centre, highlighting a significant higher risk associated to cattle; a second cluster, predominant in 2012-2016, holding the county Rosmaninhal (Castelo Branco) at the centre, for which wild boar contributed the most in relative risk. Whole-genome sequences (WGS) of 44 representative M. bovis distinguished five genetic clades and supported sustained transmission and multiple introductions in this multi-host system. Exploratory evolutionary analysis gave further support to pathogen transition between different hosts.

Comparative genomics applied to M. bovis (n=70) representing the global clonal complex diversity predicted an open pan-genome and showed diversification of discrete subpopulations through core and accessory genomes. Consistent non-synonymous SNPs illustrated clade-specific virulence landscapes correlating with disease severity. Positive selection and weaker effects of recombination compared with mutation were evidenced as predominant evolutionary forces.

Altogether, our results provide novel evidence on the population structure and evolution of M. caprae and M. bovis, delivering insights that could be used to inform adaptive TB control choices in different hosts and regions.

Publication and Meetings

Peer-review papers:

11. Ana C. Reis, Mónica V. Cunha. The open pan-genome architecture and virulence landscape of Mycobacterium bovis. Microb Genom 7, 10 (2021). doi.org/10.1099/mgen.0.000664.

10. Ana C. Reis, Mónica V. Cunha. Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis. Sci Rep 11, 18789 (2021). doi.org/10.1038/s41598-021-98226-y.

9. Ana C. Reis, Liliana C. M. Salvador, Suelee Robbe-Austerman, Rogério Tenreiro, Ana Botelho, Teresa Albuquerque, Mónica V. Cunha. Whole Genome Sequencing refines knowledge on the population structure of Mycobacterium bovis from a Multi-Host Tuberculosis System. Microorganisms 9(8), 1595 (2021). doi.org/10.3390/microorganisms9081585.

8. Ana C. Reis, Beatriz Ramos, André C. Pereira, Mónica V. Cunha. The Hard Numbers of Tuberculosis Epidemiology in Wildlife: a Meta-Regression and Systematic Review. Transbound Emerg Dis. 2020. doi: 10.1111/tbed.13948.

7. Ana C. Reis, Rogério Tenreiro, Teresa Albuquerque, Ana Botelho, Mónica V. Cunha. Long-term molecular surveillance provides clues on a cattle origin for Mycobacterium bovis in Portugal. Sci Rep 10, 20856 (2020). doi.org/10.1038/s41598-020-77713-8

6. André C. Pereira, Beatriz Ramos, Ana C. Reis, Mónica V. Cunha. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 8, 1380 (2020) doi.org/10.3390/microorganisms8091380

5. Beatriz Ramos, André C. Pereira, Ana C. Reis, Mónica V. Cunha. Estimates of the global and continental burden of animal tuberculosis in key livestock species worldwide: a meta-analysis study. One Health 10, 100169 (2020) doi.org/10.1016/j.onehlt.2020.100169.

4. Ana C. Reis, Beatriz Ramos, André C. Pereira, Mónica V. Cunha. Global trends of epidemiological research in livestock tuberculosis for the last four decades. Transbound Emerg Dis. 2020. doi.org/10.1111/tbed.13763.

3. André C. Pereira, Ana C. Reis, Beatriz Ramos, Mónica V. Cunha. Animal Tuberculosis: Impact of Disease Heterogeneity in Transmission, Diagnosis and Control. Transbound Emerg Dis. 2020. doi.org/10.1111/tbed.13539.

2. Ana C. Reis, Teresa Albuquerque, Ana Botelho, Mónica V. Cunha. Polyclonal infection as a new scenario in Mycobacterium caprae epidemiology. Vet Microbiol 2020. doi.org/10.1016/j.vetmic.2019.108533.

1. Mónica V. Cunha, Luís Miguel Rosalino, Célia Leão, Victor Bandeira, Carlos Fonseca, Ana Botelho, Ana C. Reis. Ecological drivers of Mycobacterium avium subsp. paratuberculosis infection in mongoose (Herpestes ichneumon) using IS900 as proxy. Sci Rep 10, 860 (2020) doi.org/10.1038/s41598-020-57679-3.

 

Ana C. Reis. “Comparative genomics reveals evolutionary and transmission patterns of Mycobacterium bovis from a multi-host system”. Seminar of PhD Program in Applied and Environmental Microbiology, 7 Jully 2020 (online presentation).

8th Workshop of the doctoral program in Applied and Environmental Microbiology (DP_AEM), 10 – 12 February 2020, Campus de Gualtar, University of Minho, Braga, Portugal.

7th Workshop of the doctoral program in Applied and Environmental Microbiology (DP_AEM), 24 – 27 September 2018, Campus de Gualtar, University of Minho, Braga, Portugal.

3rd Joint BIOTECnico and AEM PhD programs workshop, 11-12 June 2018, Instituto Superior Técnico, Campus Alameda, Lisbon, Portugal. (Oral presentation: Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis).

2nd Joint Workshop of the PhD programs in Applied and Environmental Microbiology (DP_AEM) and Molecular and Environmental Biology (PDBMA), 25 – 29 September 2017, Campus de Gualtar, University of Minho, Braga, Portugal. (Oral presentation: Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis).

2nd Joint BIOTECnico and AEM PhD programs workshop, 15-16 February 2017, Instituto Superior Técnico, Campus Alameda, Lisbon, Portugal. (Oral presentation: Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis).

1st Joint Workshop of the PhD Programs in Applied and Environmental Microbiology (DP_AEM) and Molecular and Environmental Biology (PDBMA), 26 – 30 September 2016, Campus de Gualtar, University of Minho, Braga, Portugal.

Oral presentations:

14. Ana C. Reis*, Mónica V. Cunha. “Insights into the evolutionary forces shaping the pan-genome architecture of strictly clonal Mycobacterium bovis”. Microbiotec21, 23 November 2021 (online presentation).

13. Ana C. Reis*, Mónica V. Cunha. “Comparative genomic analyses reveal unexpected diversity among globally distributed Mycobacterium bovis”. 7th cE3c Annual Meeting, 1 October 2021 (online presentation).

12. Ana C. Reis. Multi-Host Tuberculosis: from Pathogen Genomics to Transmission Dynamics”. BioISI Research Day 2020, 26 November 2020 (online presentation).

11. Ana C. Reis*, Liliana Salvador, Suelee Robbe-Austermann, Rogério Tenreiro, Teresa Albuquerque, Ana Botelho, Mónica V. Cunha. “Evolutionary History and Ongoing Transmission of Mycobacterium bovis in a Multi-Host System”. 6th cE3c Annual Meeting, 1-2 October 2020 (online presentation).

10. Ana C. Reis. “Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis”. Doctoral Seminar III, 17 September 2020, Faculdade de Ciências da Universidade de Lisboa, Portugal (online presentation).

9. Ana C. Reis*, Liliana Salvador, Mónica V. Cunha. “Genome-wide diversification of Mycobacterium bovis”.  Microbiotec19, 5-7 December 2019, Universidade de Coimbra, Coimbra, Portugal. Poster with flash presentation.

8. Ana C. Reis*, Liliana Salvador, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Deciphering Mycobacterium bovis phylogeny using genome-wide SNP data”. Microbiotec19, 5-7 December 2019, Universidade de Coimbra, Coimbra, Portugal. Poster with flash presentation.

7. Ana C. Reis*, Liliana Salvador, Teresa Albuquerque, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Transmissão de Mycobacterium bovis na zona epidemiológica de risco para a tuberculose em Portugal”. Wildlife Game Management Summit-Cimeira da Fauna e Gestão Cinegética, 28-29 June 2019, Oeiras, Portugal.

6. Ana C. Reis. “Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis”. Doctoral Seminar II, 24 June 2019, Faculdade de Ciências da Universidade de Lisboa, Portugal.

5. Mónica V. Cunha*, Ana C. Reis, André Pereira, Beatriz Ramos, Teresa Albuquerque, Ana Botelho. “Passado, Presente e Futuro da Investigação em tuberculose animal no INIAV, IP, em Portugal”. I Workshop Ibérico y II Nacional de investigación en Tuberculosis animal, 4 April 2019, Cáceres, Espanha.

4. Ana C. Reis*, Mónica V. Cunha. “Multi-host tuberculosis: Molecular perspective of epidemiological processes”. Encontro Scientia, 21 June 2018, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.

3. Ana C. Reis. “Systems Epidemiology to Devise New Interventions for Multi-Host Tuberculosis”. Doctoral Seminar I, 11 June 2018, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.

2. Ana C. Reis*, Teresa Albuquerque, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Bayesian analysis of the population structure of Mycobacterium bovis in a hotspot area of animal tuberculosis, Portugal”. MicroBiotec17, 7-9 December 2017, Universidade Católica Portuguesa, Porto, Portugal.

1. Ana C. Reis*, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Spatiotemporal analysis of animal-adapted members of Mycobacterium tuberculosis complex: epidemiological connections revealed by fine-scale genome analyses”. 38th annual Congress of European Society of Mycobacteriology, 25-29 June 2017, Sibenik, Croácia.

 

Poster presentations:

6. Ana C. Reis*, Rogério Tenreiro, Mónica V. Cunha. “Comparative Genomic Analyses of Field Isolates Reveals a Characteristic Architecture of Mycobacterium bovis Pan-genome”. 6th cE3c Annual Meeting, 1-2 October 2020 (online presentation).

5. Ana C. Reis*, Liliana Salvador, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Spatiotemporal dynamics of Mycobacterium bovis in Portugal: wildlife species as key players in the spread of animal TB”.  RUSI X, 18-19 October 2019, Lousã, Portugal.

4. Ana C. Reis*, Liliana Salvador, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Genome-wide diversity and phylogeography of Mycobacterium bovis in tuberculosis hotspot area”. 8th Congress of European Microbiologists (FEMS 2019), 7-11 July 2019, Glasgow, Scotland.

3. Ana C. Reis*, Liliana Salvador, Teresa Albuquerque, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “A utilização de genómica comparativa para evidenciar processos de adaptação de Mycobacterium bovis”. Wildlife Game Management Summit-Cimeira da Fauna e Gestão Cinegética, 28-29 June 2019, Oeiras, Portugal.

2. Ana C. Reis*, Teresa Albuquerque, Ana Canto, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Molecular perspective of ongoing epidemiological processes in a TB hotspot scenario, mainland Portugal”. RUSI VIII, 15-16 September 2017, Arcos de Valdevez, Portugal. 3rd award at poster category.

1. Ana C. Reis*, Teresa Albuquerque, Madalena Monteiro, Célia Leão, Ana Canto, Ana Botelho, Mónica V. Cunha. “Epidemiological inferences on concomitant infection by Mycobacterium avium subsp. paratuberculosis and Mycobacterium bovis in red deer and wild boar from Portugal”. RUSI VII, 16-17 September 2016, Universidad de Extremadura, Jarandilla de la Vera, Spain.

Outreach Publications:

10. Mónica V. Cunha, Ana C. Reis, André C. Pereira, Beatriz Ramos, Teresa Albuquerque, Ana Botelho, Nuno Santos. Tuberculose animal: diagnóstico, epidemiologia, investigação e controlo. Vida Rural out, 1851 (2019)

9. Mónica V. Cunha, Ana C. Reis, Ana Botelho, João S. Proença. Tuberculose animal em Portugal. Caça & Cães de Caça Nº 256: 40-43 (2018).

8. Mónica V. Cunha, Ana C. Reis, João S. Proença. Exame inicial de caça maior: O Edital nº1/2011. Caça & Cães de Caça Nº 256: 44-45 (2018).

7. Mónica V. Cunha, Ana C. Reis. Tuberculose animal no mundo. Caça & Cães de Caça Nº 256: 46-47 (2018).

6. Mónica V. Cunha, Ana C. Reis, Pedro Vitorino. Expansão demográfica do Javali. Caça & Cães de Caça Nº 257: 49-51 (2018).

5. Mónica V. Cunha, Ana C. Reis. Doenças infeciosas que afetam os suídeos. Caça & Cães de Caça Nº 257: 52-55 (2018).

4. Jacinto Gomes, Ana C. Reis & Mónica V. Cunha. Parasitas no javali com implicações em saúde pública. Caça & Cães de Caça Nº 257: 56-59 (2018).

3. Mónica V. Cunha, Ana C. Reis. Um outro olhar sobre a raposa e os sacarrabos. Caça & Cães de Caça Nº 258: 24-25 (2018).

2. Mónica V. Cunha, Ana C. Reis. Vírus e parasitas de carnívoros silvestres. Caça & Cães de Caça Nº 258: 26-29 (2018).

1.  Mónica V. Cunha, Ana C. Reis. Bacterioses dos carnívoros silvestres. Caça & Cães de Caça Nº 258: 30-31 (2018).

Training

International Symposium and Workshop on “Principles and dynamics governing transmission of mycobacterial infection”, with credit 1ECTS. 22-24 May 2018, Wageningen Institute of Animal Sciences, Wageningen, The Netherlands.

Advanced course “Survey for ArcGIS”, 17 April 2019. Internal training INIAV.

Advanced course “Collector for ArcGIS”, 16 April 2019. Internal training INIAV.

Advanced course “ArcMap 1: Iniciação ao SIG”, 4 December 2018. Internal training INIAV.

Advanced training in Bionumerics 6.6, with the duration of 6 hours. May 2018, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.

Advanced course: “Fitting geostatistical and spatial point process models to spatial survey data”, with the duration of 20 hours, by Center of Statistics and Applications at Faculty of Sciences, University of Lisbon, Portugal (May 2018).

Advanced course: “Short Short course on Spatial and Spatio-temporal Bayesian Models with R”, with the duration of 14 hours, by Center of Statistics and Applications at Faculty of Sciences, University of Lisbon, Portugal (June 2017).

Advanced course “R without fear: an R course in evolutionary ecology”, with the duration of 36 hours, by cE3c at Faculty of Sciences, University of Lisbon, Portugal (November 2016).


 

Scientific dissemination for general public:

Collaborator at 5º Encontro de Negaceiros e Caçadores de Pombos Torcazes, 28 Setembro 2019, Arraiolos, Portugal.

Collaborator at Feira de Caça, Pesca, Turismo e Natureza, 5-7 Julho 2019, Albufeira, Portugal.

Collaborator at Expocaça – Feira Internacional da Caça e Armas, 3-5 Maio 2019, Santarém, Portugal.

 

 

Workshop on transferable skills: Self-knowledge, balance of competences, customized and effective CV, preparation for selection interviews, with Dr. Cátia Marques. 11-12 February 2020, University of Minho, Braga, Portugal.

Communication Skills (course level 1), by Dr. Ana Salgado, 30 September 2016, University of Minho, Braga, Portugal.

Communication Skills (course level 2), by Dr. Ana Salgado, 28 September 2017, University of Minho, Braga, Portugal.

 

Awards

FEMS attendance grant (FEMS Congress 2019).

3rd award in poster presentation category (Ana C. Reis, Teresa Albuquerque, Ana Canto, Ana Botelho, Rogério Tenreiro, Mónica V. Cunha. “Molecular perspective of ongoing epidemiological processes in a TB hotspot scenario, mainland Portugal”. RUSI VIII, 15-16 September 2017, Arcos de Valdevez, Portugal).

 

Current job position:

Research scholarship | July 2021 – Present

Team member of the research project “SARS-Control: Avaliação dos impactos de SARS-CoV-2 no ciclo urbano da água e dos efeitos a jusante em Saúde Pública” (ref. LISBOA-01-02B7-FEDER-070076), funded by Fundo Europeu de Desenvolvimento Regional (FEDER), Programa Operacional Regional de Lisboa