Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

The global burden of rheumatic heart disease (RHD) has triggered a World Health Organization response to drive forward development of a vaccine against the causative human pathogen Streptococcus pyogenes . This burden stems primarily from low- and middle-income settings where there are high levels of S. pyogenes skin and soft tissue infections, which can lead to RHD.

Invasive non-typhoidal Salmonella (iNTS) disease continues to be a significant public health problem in sub-Saharan Africa. Common clinical misdiagnosis, antimicrobial resistance, high case fatality and lack of a vaccine make iNTS a priority for global health research. Using whole genome sequence analysis of 164 invasive Salmonella isolates obtained through population-based surveillance between 2008 and 2016, we conducted genomic analysis of the serovars causing invasive Salmonella diseases in rural Gambia. The incidence of iNTS varied over time. The proportion of atypical serovars causing disease increased over time from 40 to 65 % compared to the typical serovars Enteritidis and Typhimurium that decreased from 30 to 12 %. Overall iNTS case fatality was 10%, but case fatality associated with atypical iNTS alone was 10 %. Genetic virulence factors were identified in 14/70 (20 %) typical serovars and 45/68 (66 %) of the atypical serovars and were associated with: invasion, proliferation and/or translocation (Clade A); and host colonization and immune modulation (Clade G). Among Enteritidis isolates, 33/40 were resistant to four or more of the antimicrobials tested, except ciprofloxacin, to which all isolates were susceptible. Resistance was low in Typhimurium isolates, but all 16 isolates were resistant to gentamicin. The increase in incidence and proportion of iNTS disease caused by atypical serovars is concerning. The increased proportion of atypical serovars and the high associated case fatality may be related to acquisition of specific genetic virulence factors. These factors may provide a selective advantage to the atypical serovars. Investigations should be conducted elsewhere in Africa to identify potential changes in the distribution of iNTS serovars and the extent of these virulence elements.

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Introduction: Healthcare-associated infections (HAIs) are better documented in developed than in developing countries. There are emerging reports regarding the high frequency of HAIs in developing countries. We aimed to report an outbreak of an HAI caused by Serratia liquefaciens at a rural health center in The Gambia. Methodology: Following an abrupt increase in the isolation of S. liquefaciens in clinical samples, laboratory and clinical consumables, as well as staff, were screened for contamination with S. liquefaciens. Conventional microbiological techniques and biochemical identification tests were used. A phenotypic typing was achieved using the Kirby-Bauer antibiotic susceptibility method. Strategies to control the outbreak were implemented. Results: A total of 794 samples were processed during the outbreak; 44 (6%) grew S. liquefaciens. Five (25%) of the 20 suspected contaminated materials (hospital consumables and equipment) screened yielded growth of the organism. The primary source of the outbreak was hospital consumables. Three (7%) of the 44 infected children died with no other known cause than S. liquefaciens infection. Ninety-nine percent similarity of the antibiogram phenotypic typing suggests the isolates were from the same clonal origin. The outbreak was successfully controlled after the removal and sterilization of the respective contaminated fluids and equipment. Conclusions: This HAI was caused by poor practice in the preparation of medications for nebulization and intravenous infusion, hygiene practices, and a lack of awareness among staff about infection control. We recommend further studies to delineate the role played by HAIs in the developing world.