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Determining the epidemiology and molecular evolution of antimicrobial drug resistance in Cape Verde

  • Full or part time

    Prof Marco Rinaldo Oggioni
  • Application Deadline
    Sunday, January 12, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Cape Verde is an archipelago located 450 km off the coast of Senegal, that was found uninhabited by the Portuguese in the mid-15th century. The southern islands were populated first with European immigrants and enslaved Africans from the neighbouring coast. Two centuries later, after the decline of the slave trade, there was a movement of people towards the islands of the north. Due to its geographic isolation, unique history of colonisation (serial founder effects), strong communication with other countries through recent migration and tourism, and finally, a dry climate that prevents the spread of major tropical disease, the archipelago of Cape Verde provides a unique model for the study of the natural history of infectious disease and evolution of antimicrobial drug resistance (AMR) caused by microorganisms that are widespread across the world. We have established two funded research programmes in these areas. The first project aims to study the epidemiology and genomics of host-pathogen interactions underlying susceptibility to the stomach–colonizing bacterium Helicobacter pylori. H. pylori infection is the most common infection in the world and causes peptic ulcer and gastric cancer; gastric cancer is the second cause of death from malignancy. Preliminary results from our work indicate that the prevalence of infection in the general population is ~84%, and that the bacterial genomes derive ancestry from both European and African continents. The level of AMR of the strains collected to four antibiotics is high and we observed cases of multidrug resistance. We also observe multiple infections within the same host, which differ in the antibiotic resistance pattern: there are both susceptible and resistance strains inhabiting the same stomach.

In the second project, we collated data on AMR between 2013 and 2017 from the records of the Northern and Southern central hospitals in Cape Verde. We observed an increase in resistance levels of Staphylococcus aureus strains throughout the years across the archipelago in Cape Verde. S. aureus is a common colonizer of the anterior nares of the nose, the skin and of other mucosa; but S. aureus strains can cause important infections in the community and in the hospital. We have found a lineage in S. aureus with a unique pattern of antibiotic resistance.

To evaluate the origin and molecular evolution of AMR in H. pylori and S. aureus in Cape Verde, we have obtained whole-genome sequences of both susceptible and resistant strains. The specific objectives are:

1. To perform genome-wide association analyses to identify new genetic variants and genes associated with differences of susceptibility to antibiotics in H. pylori. The resistance patterns observed are not fully explained by resistance variants already described. The dataset composed by >220 sequenced strains characterized for antibiotic resistance levels will allow to perform phenotype-genotype correlations and to evaluate the genetic architecture of AMR in H. pylori in Cape Verde.

2. To identify the genetic elements that give rise to both the common and unique pattern of antibiotic resistance in S. aureus in Cape Verde. To annotate known genetic variants of resistance and to perform genome-wide analyses of the diversity of the resistant strains.

3. To evaluate the genetic diversity and evolution of H. pylori and S. aureus strains across the Cape Verde. To characterize the genetic variation and to perform population genetics analyses in both susceptible and resistant strains to evaluate the role of the population history (serial founder effects) of the archipelago and of the action of the antibiotic selective pressure in the distribution of the genetic diversity of H. pylori and S. aureus strains across the archipelago.

To understand within-the-host evolution of AMR in H. pylori. To characterize the genetic variation and to perform population genetics analyses of strains with different AMR patterns colonizing the same stomach.


UK/EU applicants only.

Entry requirements:

Applicants are required to hold/or expect to obtain a UK Bachelor Degree 2:1 or better in a relevant subject.

The University of Leicester English language requirements apply where applicable:

How to apply:

Please refer to the application guidance and apply using the online application link at

Project / Funding Enquiries:
Application enquiries to
Closing date for applications: Sunday 12th January 2020

Funding Notes

4 year MIBTP studentship offering

Stipend at UKRI rates

Tuition fees at UK/EU rates

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