Understanding the mechanisms of transmission of human leptospirosis in slums settlements in Salvador, Brazil

Leptospirosis, a spirochetal zoonosis, has emerged as an important health problem as slum settlements have expanded rapidly worldwide and created conditions for rat-borne transmission. In Brazil, 12,000 individuals are annually infected with leptospirosis, with a death rate of about 12%. In the city of Salvador, Brazil, where transmission mostly occurs in peridomestic environments, the government-led expansion of closed sewer networks has  resulted in a significant decrease of infection rates for leptospirosis. 

However, due to political neglect and the uncontrolled expansions of slums, construction of conventional governmentally led closed sewer systems (GOV-INT) is increasingly problematic. To address this issue, innovative and more economical methods that require of community residents involvement (COM-INT) have emerged as suitable alternatives to improve sanitation in slum settlements. However, assessing the real impact of sanitation intervention, such as GOV-INT and COM-INT, is problematic because of methodological issues due to confounding factors and difficulties with randomization of the population to obtain large enough large sample sizes.

Current knowledge gaps

To the best of our knowledge, no study has been carried out to assess the potentially positive effects of COM-INT on the reduction of leptospirosis risk. Based on preliminary descriptive statistics from an ongoing study in Salvador, to which this project directly contributes, it has been conjectured that GOV-INT and COM-IN are equally effective in the reduction of Leptospirosis infections. In this context, the use of spatio-temporal statistical methods are crucial in order to infer the actual impact of COM-INT by taking account of both measured and unmeasured risk factors of Leptospirosis infection.

Study aims

  1. Determine the mechanisms by which COM-INT and GOV-INT reduce direct human contact with sewage and environmental pathogen load in urban slums.
  2. Determine the contribution of COM-INT and GOV-INT on a decline in severe disease incidence in a large urban center.

Study design/methodology

As part of a Wellcome-Trust project, this study  will be split into the following two parts (each referring to the above aims in turn)

  1. The main cause of Leptospira infection is exposure to contaminated sewage and run-off. Hence, to pursue the first study aim, statistical methods that combine information from environmental reservoirs and resident’s movement will be fitted to data from an ongoing study in the community of Marechal Rodon in Salvador, Brazil. This study site consists of 9 areas, 3 with GOV-INT, 3 with COM-INT and 3 with no intervention. A total of 2,582 soils samples will be collected and tested for Leptospira DNA, before and after the interventions. These data will be integrated with human mobility data collected on 150 individuals using multifunctional sensor nodes to quantity the exposure to contamination sources

A secondary spatio-temporal geostatistical analysis will be conducted to assess the effectiveness of COM-INT and GOV-INT, using data collected since 1996 from a hospital-based surveillance for leptospirosis that covers the population of Salvador since. To account for confounding effects, information on socio-economic and environmental factors will also be incorporated into the spatio-temporal model.


T1 – Basic Research

The project is expected to generate at least 3 papers in an international refereed epidemiology and public health journal. It will also provide much needed research on the impact of GOV-INT and COM-INT transmission. Recommendations for the implementation of COM-INT in the study area and in urban slum areas in Brazil will be made.

In addition to the statistical training provided by the primary supervisor Dr Giorgi, training in field epidemiology, ecology and zoonotic diseases transmission and prevention strategies specific to the slum settlement context in Salvador will be provided by supervisor Federico Costa at Fiocruz and the Federal University of Bahia, Brazil.

The student is expected to:

1. have a strong interest in the application of advanced modern statistical methods to address public health challenges;

2. be able to autonomously learn new statistical methods and how they are used in open-source statistical software;

3. be able to communicate and work in a multidisciplinary team.


Eyre, M. T., Carvalho-Pereira, T. S., Souza, F. N., Khalil, H., Hacker, K. P., Serrano, S., Taylor, J. P., Reis, M. G., Ko, A. J., Begon, M., Diggle, P. J., Costa, F., Giorgi, E. (2020) A multivariate geostatistical framework for combining multiple indices of abundance for disease vectors and reservoirs: A case study of rattiness in a low-income urban Brazilian community. Journal of the Royal Interface. DOI:10.1098/rsif.2020.0398

Diggle, P. J., Giorgi, E. (2019) Model-based geostatistics for global public health: Methods and applications. CRC/Chapman & Hall

Hacker KP, Sacramento GA, Cruz JS, De Oliveira D, Nery N, Lindow JC, Carvalho M, Hagan J, Diggle PJ, Begon M, Reis MG, Wunder EA, Ko AI, Costa F. (2020) Influence of Rainfall on Leptospira Infection and Disease in a Tropical Urban Setting, Brazil. Emerging Infectious Diseases. DOI: 10.3201/eid2602.190102

Casanovas-Massana A, Costa F, Riediger IN, Cunha M, de Oliveira D, Mota DC, Sousa E, Querino VA, Nery N Jr., Reis MG, Wunder EA Jr., Diggle PJ, Ko AI (2017). Spatial and temporal dynamics of pathogenic Leptospira in surface waters from the urban slum environment. Water Research. DOI 10.1016/j.watres.2017.11.068

Hagan JE, Moraga P, Costa F, Capian N, Ribeiro GS, Wunder Jr EA,  Felzemburgh RDM, Reis RB, Nery N, Santana FS, Fraga D, dos Santos BL, Santos AC, Queiroz A, Tassinari W, Carvalho MS, Reis MG, Diggle PJ, Ko AI. (2016) Spatiotemporal determinants of urban leptospirosis transmission: Four-year prospective cohort study of slum residents in Brazil. PLoS Negl Trop Dis. DOI: 10.1371/journal.pntd.0004275

Deadline: Thursday 11th February 2021; 12:00 noon GMT

Further details on the MRC/DTP and CASE programmes and application guidance and process can be found here