Investigating laboratory capacity and whole genome sequencing practices to inform standardised protocols for bacterial genomic surveillance in Africa.

In many parts of the world, a fever in a newborn is a medical emergency that requires immediate and precise action. When a baby develops sepsis, a severe reaction to an infection that can spread through the bloodstream, the specific type of bacteria causing the illness determines the best course of treatment. One particular bacterium, known as Klebsiella pneumoniae, is a leading cause of these dangerous infections across Africa. To stop these infections from spreading and to ensure doctors use the right medicines, scientists need to know exactly which strains of bacteria are present and how they behave. For decades, identifying these germs relied on growing them in a dish and watching how they reacted to chemicals, a process that takes time and often lacks detail. Today, a more powerful tool called whole genome sequencing has emerged. This method reads the complete genetic code of a bacterium, offering a detailed map that reveals not just what the germ is, but also how it might resist antibiotics and where it came from. Using this technology to track infections could save lives, but only if the laboratories that perform the work are equipped to handle it.

A team of researchers set out to understand the current reality of this technology across the African continent. They wanted to know if hospitals and research centers had the necessary tools and skills to move from traditional testing to this advanced genetic surveillance. To find the answer, they sent a detailed questionnaire to a wide network of clinicians and scientists in twenty-five different African countries. The goal was to map out the landscape of laboratory capacity, focusing specifically on the steps required to identify bacteria and analyze their genetic material. The survey gathered responses from fifty-two institutions, providing a clear picture of what is happening on the ground today.

The results revealed a mixed picture of capability and need. Among the institutions that answered questions about their testing abilities, sixty-one percent reported that they perform blood cultures, a process where blood is drawn from a patient and placed in a special container to encourage any bacteria to grow. Once the bacteria grow, they must be identified. Most of these laboratories, seventy-one percent, still rely on manual systems that use chemical reactions to determine the species of the bacteria. Similarly, eighty-two percent use a traditional method involving small paper disks soaked in antibiotics to see which medicines stop the bacteria from growing. While these methods are established, they are slower and less detailed than modern genetic approaches. The physical equipment in these labs is surprisingly robust in some areas; nearly every respondent reported having access to a freezer capable of reaching extremely low temperatures, a centrifuge to spin samples, and a machine to amplify genetic material. However, a specific type of incubator that gently shakes samples to help them grow was less common, available in only sixty-seven percent of the facilities.

When the researchers asked about the ability to perform whole genome sequencing, the findings showed that more than half of the respondents, fifty-four percent, can handle the entire process inside their own walls. This workflow involves extracting the genetic material from the bacteria, preparing it for reading, and then running the sequencing machine. Most of these labs, eighty-eight percent, extract the DNA themselves, primarily using kits that rely on columns to filter and purify the genetic material. As the process moves toward the later stages, such as analyzing the massive amounts of data produced by the sequencing machines, reliance on outside help increases. This highlights a significant bottleneck: while the physical sequencing is happening, the ability to interpret the results is struggling. Every single respondent who answered the question about bioinformatics reported facing challenges. They cited a lack of access to powerful computers capable of handling complex data and a shortage of space to store the digital files.

The study concludes that there is a solid foundation of capacity to support genomic surveillance for neonatal sepsis across the participating institutions. The ability to grow bacteria and even sequence their genomes exists in more than half of the surveyed labs. However, the path to using this technology to its full potential is not yet clear. The researchers found that significant investments are still needed to strengthen blood culture programs, secure reliable supply chains for the necessary materials, expand sequencing capabilities, and build the digital infrastructure required to analyze and share the data. These findings will help guide the creation of standardized protocols that fit the diverse realities of laboratories across the continent, ensuring that the promise of genetic surveillance can eventually protect the most vulnerable patients.