Infectious Disease Surveillance at CHU de Fann: Impact and Perspectives of the AFROSCREEN Project
Infectious Disease Surveillance at CHU de Fann: Impact and Perspectives of the AFROSCREEN Project
Dr. Fatoumata DIALLO (left) and Mame Salane THIAM (right)
Discover the interview with Mame Salane THIAM, a bioinformatics specialist in the bacteriology laboratory at CHU de Fann, and Dr. Fatoumata DIALLO, a medical biologist at the bacteriology-virology laboratory at CHU de Fann since 2018. She is also an assistant professor at Cheikh Anta Diop University in Dakar, in the medical bacteriology department.
Question: Can you tell us about the laboratory, how it operates, and its activities?
Mame Salane THIAM: The bacteriology laboratory is located at CHU de Fann. We carry out bacteriological analyses and, in the field of molecular biology, we focus on research related to COVID-19 and tuberculosis. For COVID-19, we detect the presence of the virus. For tuberculosis, we use the GeneXpert test to identify the disease and assess resistance to rifampicin. We also perform DNA extraction because we plan to begin sequencing tuberculosis strains, particularly from patients living with HIV. This project is funded by Germany and aims to better understand resistance mechanisms and identify new therapeutic molecules.
Dr. Fatoumata DIALLO: The COVID-19 pandemic and the AFROSCREEN project played a key role in developing our diagnostic capacities. Before the pandemic, our lab focused on bacteriology and virology. With COVID-19, we established a molecular biology laboratory, supported by AFROSCREEN, and began diagnosing the virus through PCR testing. We later expanded our activities by acquiring multiplex PCR kits, allowing us to detect up to 33 respiratory pathogens.
What has AFROSCREEN contributed?
Mame Salane THIAM: The AFROSCREEN project has greatly enriched our work. I was able to attend a bioinformatics training, especially on the GeVarLi tool, which allowed me to analyze the sequenced strains in our lab. Thanks to this tool, we processed 100 sequenced COVID-19 strains and identified the different circulating variants. This enabled us to build a phylogenetic tree and submit these sequences to the GISAID database.
Dr. Fatoumata DIALLO: AFROSCREEN has been extremely beneficial. It allowed us to equip our lab with a MiSeq sequencer (provided by the Ministry of Health but used thanks to AFROSCREEN), as well as an iSeq, a Qubit for nucleic acid quantification, refrigerators for reagents, and more. The project strengthened our diagnostic capacities not only for COVID-19 but also for other respiratory diseases. We also received specialized training, including a sequencing course in Abidjan in 2022.
In your opinion, what is the future of bioinformatics in respiratory disease surveillance in West Africa and more broadly?
Mame Salane THIAM: Bioinformatics is essential because it allows for fast and efficient data analysis. It also helps us fully leverage sequencing by identifying important mutations and monitoring the evolution of pathogens in real time.
Dr. Fatoumata DIALLO: Disease surveillance and sequencing are critical. We need to strengthen bioinformatics training to be autonomous in analyzing sequencing data. Building phylogenetic trees and understanding pathogen transmission are key elements for improving epidemic management.
Do you have additional needs to further develop the Fann lab’s capacities?
Mame Salane THIAM: In addition to sequencing collaboration, we have a critical need for data storage infrastructure. Currently, we store sequences on an external hard drive, which is far from ideal. Acquiring a NAS server would be essential to securely and centrally store our data. Lastly, we need more reagents and equipment to continue developing our diagnostic capacities.
Do you think the One Health concept plays a role in your work?
Dr. Fatoumata DIALLO: Yes, it’s fundamental. The interactions between human, animal, and environmental pathogens require an integrated approach. The COVID-19 example clearly shows that surveillance must be global to anticipate the emergence of new epidemics.
Mame Salane THIAM: In terms of bioinformatic data processing, there isn’t a big difference between human and animal samples. We use the same analysis tools. For example, HIV research has traced its origins to monkeys, which shows how important bioinformatics is for understanding the links between human and animal health.
What are the prospects for 2025?
Dr. Fatoumata DIALLO: We want to expand sequencing to other pathogens, including bacteria, to study antimicrobial resistance. We currently have several bacterial strains waiting to be sequenced to study their resistance genes, which could directly impact how infections are managed in hospitals.
We also want to work on sequencing hepatitis B viruses and other respiratory infections. Moreover, we are preparing several publications based on AFROSCREEN analyses: a first article on circulating COVID-19 variants in 2022 is being finalized, followed by two others on our genomic surveillance work.
Dr. Fatoumata DIALLO (left) and Mame Salane THIAM (right)
Discover the interview with Mame Salane THIAM, a bioinformatics specialist in the bacteriology laboratory at CHU de Fann, and Dr. Fatoumata DIALLO, a medical biologist at the bacteriology-virology laboratory at CHU de Fann since 2018. She is also an assistant professor at Cheikh Anta Diop University in Dakar, in the medical bacteriology department.
Question: Can you tell us about the laboratory, how it operates, and its activities?
Mame Salane THIAM: The bacteriology laboratory is located at CHU de Fann. We carry out bacteriological analyses and, in the field of molecular biology, we focus on research related to COVID-19 and tuberculosis. For COVID-19, we detect the presence of the virus. For tuberculosis, we use the GeneXpert test to identify the disease and assess resistance to rifampicin. We also perform DNA extraction because we plan to begin sequencing tuberculosis strains, particularly from patients living with HIV. This project is funded by Germany and aims to better understand resistance mechanisms and identify new therapeutic molecules.
Dr. Fatoumata DIALLO: The COVID-19 pandemic and the AFROSCREEN project played a key role in developing our diagnostic capacities. Before the pandemic, our lab focused on bacteriology and virology. With COVID-19, we established a molecular biology laboratory, supported by AFROSCREEN, and began diagnosing the virus through PCR testing. We later expanded our activities by acquiring multiplex PCR kits, allowing us to detect up to 33 respiratory pathogens.
What has AFROSCREEN contributed?
Mame Salane THIAM: The AFROSCREEN project has greatly enriched our work. I was able to attend a bioinformatics training, especially on the GeVarLi tool, which allowed me to analyze the sequenced strains in our lab. Thanks to this tool, we processed 100 sequenced COVID-19 strains and identified the different circulating variants. This enabled us to build a phylogenetic tree and submit these sequences to the GISAID database.
Dr. Fatoumata DIALLO: AFROSCREEN has been extremely beneficial. It allowed us to equip our lab with a MiSeq sequencer (provided by the Ministry of Health but used thanks to AFROSCREEN), as well as an iSeq, a Qubit for nucleic acid quantification, refrigerators for reagents, and more. The project strengthened our diagnostic capacities not only for COVID-19 but also for other respiratory diseases. We also received specialized training, including a sequencing course in Abidjan in 2022.
In your opinion, what is the future of bioinformatics in respiratory disease surveillance in West Africa and more broadly?
Mame Salane THIAM: Bioinformatics is essential because it allows for fast and efficient data analysis. It also helps us fully leverage sequencing by identifying important mutations and monitoring the evolution of pathogens in real time.
Dr. Fatoumata DIALLO: Disease surveillance and sequencing are critical. We need to strengthen bioinformatics training to be autonomous in analyzing sequencing data. Building phylogenetic trees and understanding pathogen transmission are key elements for improving epidemic management.
Do you have additional needs to further develop the Fann lab’s capacities?
Mame Salane THIAM: In addition to sequencing collaboration, we have a critical need for data storage infrastructure. Currently, we store sequences on an external hard drive, which is far from ideal. Acquiring a NAS server would be essential to securely and centrally store our data. Lastly, we need more reagents and equipment to continue developing our diagnostic capacities.
Do you think the One Health concept plays a role in your work?
Dr. Fatoumata DIALLO: Yes, it’s fundamental. The interactions between human, animal, and environmental pathogens require an integrated approach. The COVID-19 example clearly shows that surveillance must be global to anticipate the emergence of new epidemics.
Mame Salane THIAM: In terms of bioinformatic data processing, there isn’t a big difference between human and animal samples. We use the same analysis tools. For example, HIV research has traced its origins to monkeys, which shows how important bioinformatics is for understanding the links between human and animal health.
What are the prospects for 2025?
Dr. Fatoumata DIALLO: We want to expand sequencing to other pathogens, including bacteria, to study antimicrobial resistance. We currently have several bacterial strains waiting to be sequenced to study their resistance genes, which could directly impact how infections are managed in hospitals.
We also want to work on sequencing hepatitis B viruses and other respiratory infections. Moreover, we are preparing several publications based on AFROSCREEN analyses: a first article on circulating COVID-19 variants in 2022 is being finalized, followed by two others on our genomic surveillance work.