Zoonoses, Infectious Diseases and Antimicrobial Resistance

Welcome to my personal website. I have organised my work by themes in the project dropdown menu in the navigation bar. I will post in progress work to this page alongside completed work. In progress work will be labelled as such.

My work is organised into three themes:

  1. Lassa fever, including assay development, epidemiology and rodent ecology
  2. Research on COVID-19, specifically the interaction between cigarette smoking and SARS-CoV-2/COVID-19 infection, severity and mortality
  3. A one health approach to antimicrobial resistance particularly within the poultry industry

I have recentyl completed my PhD upgrading process, the report I produced for this is available here

Lassa fever

Lassa mammarenavirus assay development

In progress

Diagnostics for Lassa mammarenavirus (LASV) are challenging due to the variability in viral sequence and structure. Several commercial PCR and antibody kits are available. To our knowledge there no pan-species antibody assays. To support our ongoing work on understanding the epidemiology and transmission dynamics in multi-species systems in endemic regions we have begun developing a cross-species assay. We adopted an approach that has been found to be successful for Peste des petits ruminants a virus that affects goats, sheep and camels and is targeted for eradication. These assays are built on the Luciferase Immunoprecipitation System (Berguido et al. 2016) which detect the presence of antibodies against the presented antigen.

Our work so far in the development of the assay is presented in the following posts:

Rodent ecology and zoonoses studies in West Africa

In progress

I am in the process of conducting a scoping review to consolidate prior research that has involved the trapping of individual rodents in the WHO West Africa region. I have made my initial results available below. I will continue to develop this and produce a data resource to accompany this work.

I have summarised the data from studies identified for this review and made it explorable through an RShiny application. The app is currently a work in progress but is available here if you have any comments on the app or would be interested in seeing the data explored slightly differently please don’t hesitate to contact me.

Rodent trapping to inform a dynamic rodent assemblage and population model in Eastern Sierra Leone

Ongoing work

A pilot study has been performed to inform a planned 2 year programme of repeat trapping in several settings in Sierra Leone. This pilot study was presented as a poster at the Planetary Health Annual Meeting.

Data collection for the longitudinal study began in April 2021

The niche of One Health approaches in Lassa fever surveillance and control (Arruda et al. 2021)

Lassa fever (LF), a zoonotic illness, represents a public health burden in West African countries where the Lassa virus (LASV) circulates among rodents. Human exposure hinges significantly on LASV ecology, which is in turn shaped by various parameters such as weather seasonality and even virus and rodent-host genetics. Furthermore, human behaviour, despite playing a key role in the zoonotic nature of the disease, critically affects either the spread or control of human-to-human transmission. Previous estimations on LF burden date from the 80s and it is unclear how the population expansion and the improvement on diagnostics and surveillance methods have affected such predictions. Although recent data have contributed to the awareness of epidemics, the real impact of LF in West African communities will only be possible with the intensification of interdisciplinary efforts in research and public health approaches. This review discusses the causes and consequences of LF from a One Health perspective, and how the application of this concept can improve the surveillance and control of this disease in West Africa.


COVID-19 transmission and control strategies

The COVID-19 pandemic is an example of the potential impact from emerging zoonotic infectious diseases. During the early stages of the pandemic I supported CMMID at LSHTM with their data management pipeline and was a member of the COVID-19 working group. As case numbers in the UK increased after the summer I reduced my role in the epidemiological and modelling work to increase the amount of time I could contribute to the clinical response.

COVID-19 and the association with smoking

Since March 2020 I have also been involved in a project investigating the association of smoking and SARS-CoV-2 infection, and COVID-19 severity and mortality. This work has been led by Olga Perski and colleagues at UCL-Tobacco and Alcohol Research Group.

Current and former smoking is associated with worse outcomes and increased rates of hospitalisation from respiratory infections such as Respiratory Synciatial Virus, Influenza viruses and bacterial infections. Because of this there was an early concern about how the pandemic caused by SARS-CoV-2 may interact with smoking.

Early data released from healthcare services in China in the early parts of 2020 suggested that smoking was not a significant risk factor for COVID-19 disease. Whether this was a true effect or reflected poor recording or reporting was unclear. We began to synthesise the published and pre-print literature to investigate the specific association of smoking and COVID-19. This was initially performed as a report for the Royal College of Physicians, London and was expanded following a request from Public Health England.

Quit for COVID

Figure 1: Quit for COVID

Other work

Another group that were potentially at greater risk of adverse outcomes from COVID-19 infection were individuals suffering with Sickle Cell Disease. We wrote a commentary piece to draw attention to this group of individuals who are more prevalent in sub-Saharan countries in Africa that also suffer from a further burden of often under-developed healthcare infrastructure (Dexter et al. 2020)

Along with colleagues from the PANDORA network we tried to identify the countries that could be at greatest risk of importation of cases early in the epidemic based off flight data (Haider et al. 2020)

AMR and Chickens

I have been involved in two recently published studies investigating the prevalence of AMR in chicken farms in Malaysia. This work has been led by Abdinasir Osman (ORCiD) and Sharifo Ali-Elmi (ORCiD).

  1. Antimicrobial Resistance Patterns and Risk Factors Associated with Salmonella spp. Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross-Sectional Study. Available from pathogens.
  2. Identification of Risk Factors Associated with Resistant Escherichia coli Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross Sectional Study. Availables from antibiotics.
Arruda, Liã Bárbara, Najmul Haider, Ayodeji Olayemi, David Simons, Deborah Ehichioya, Adesola Yinka-Ogunleye, Rashid Ansumana, et al. 2021. “The Niche of One Health Approaches in Lassa Fever Surveillance and Control.” Annals of Clinical Microbiology and Antimicrobials 20 (1): 1–12.
Berguido, Francisco J., Sanne Charles Bodjo, Angelika Loitsch, and Adama Diallo. 2016. “Specific Detection of Peste Des Petits Ruminants Virus Antibodies in Sheep and Goat Sera by the Luciferase Immunoprecipitation System.” Journal of Virological Methods 227 (January): 40–46. https://doi.org/10.1016/j.jviromet.2015.10.008.
Dexter, Daniel, David Simons, Charles Kiyaga, Nathan Kapata, Francine Ntoumi, Richard Kock, and Alimuddin Zumla. 2020. “Mitigating the Effect of the COVID-19 Pandemic on Sickle Cell Disease Services in African Countries.” The Lancet Haematology 7 (6): e430–32. https://doi.org/10.1016/S2352-3026(20)30122-8.
Haider, Najmul, Alexei Yavlinsky, David Simons, Abdinasir Yusuf Osman, Francine Ntoumi, Alimuddin Zumla, and Richard Kock. 2020. “Passengers’ Destinations from China: Low Risk of Novel Coronavirus (2019-nCoV) Transmission into Africa and South America.” Epidemiology & Infection 148. https://doi.org/10.1017/S0950268820000424.



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