The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times 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 illuminate 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 reemerging 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 evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Patent Ductus Arteriosus in Preterm Infants: Do We Have the Right Answers?

Patent ductus arteriosus (PDA) is a common clinical condition in preterm infants. Preterm newborns with PDA are at greater risk for several morbidities, including higher rates of bronchopulmonary dysplasia (BPD), decreased perfusion of vital organs, and mortality. Therefore, cyclooxygenase (COX) inhibitors and surgical interventions for ligation of PDA are widely used. However, these interventions were reported to be associated with side effects. In the absence of clear restricted rules for application of these interventions, different strategies are adopted by neonatologists. Three different approaches have been investigated including prophylactic treatment shortly after birth irrespective of the state of PDA, presymptomatic treatment using echocardiography at variable postnatal ages to select infants for treatment prior to the duct becoming clinically significant, and symptomatic treatment once PDA becomes clinically apparent or hemodynamically significant. Future appropriately designed randomized controlled trials (RCTs) to refine selection of patients for medical and surgical treatments should be conducted. Waiting for new evidence, it seems wise to employ available clinical and echocardiographic parameters of a hemodynamically significant (HS) PDA to select patients who are candidates for medical treatment. Surgical ligation of PDA could be used as a back-up tool for those patients who failed medical treatment and continued to have hemodynamic compromise

Role of serum (1,3)‐β‐d‐glucan assay in early diagnosis of invasive fungal infections in a neonatal intensive care unit

Objectives: To study the microbiological pattern of late onset neonatal sepsis cultures and to assess the diagnostic performance of serum (1,3)‐β‐d‐glucan level for early diagnosis of invasive fungemia in high‐risk infants admitted to a neonatal intensive care unit. Methods: A prospective multicenter clinical trial conducted on infants at high risk for invasive fungal infections, with suspected late onset sepsis, admitted to a neonatal intensive care unit at Mansoura University Children's Hospital and Mansoura General Hospital between March 2014 and February 2016. Results: A total of 77 newborn infants with high risk of invasive fungal infection were classified based on blood culture into three groups: no fungemia (41 neonates with proven bacterial sepsis), suspected fungemia (25 neonates with negative blood culture), and definite fungemia group (11 neonates with culture‐proven Candida). The growing organisms were Klebsiella spp. (14/54); Escherichia coli (12/54); Staphylococcus spp. (12/54; coagulase‐negative Staphylococcus [9/54]; Staphylococcus aureus [3/54]); Pseudomonas aerouginosa (3/54); and Proteus spp. (2/54). Moreover, 11/54 presented Candida. Serum (1,3)‐β‐d‐glucan concentration was significantly lower in the no fungemia group when compared with the definite fungemia group. The best cut‐off value of (1,3)‐β‐d‐glucan was 99 pg/mL with sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 63.6%, 95.1%, 77.8%, 90.7%, and 88.5%, respectively. Conclusion: (1,3)‐β‐d‐glucan assay has a limited sensitivity with excellent specificity and negative predictive value, which allow its use as an aid in exclusion of invasive neonatal fungal infection. Accurate diagnosis and therapeutic decisions should be based on combining (1,3)‐β‐d‐glucan assay with other clinical, radiological, and microbiological findings. Resumo: Objetivos: Estudar o padrão microbiológico das culturas de sepse neonatal de início tardio e avaliar o desempenho diagnóstico do nível de (1,3)‐β‐D‐glucano no soro para diagnóstico precoce de fungemia invasiva em neonatos de alto risco internados em uma unidade de terapia intensiva neonatal. Métodos: Ensaio clínico multicêntrico prospectivo conduzido em neonatos internados em uma unidade de terapia intensiva neonatal com suspeita de sepse de início tardio que estavam em risco de infecções fúngicas invasivas no hospital universitário infantil de Almançora e no hospital geral de Almançora entre março de 2014 e fevereiro de 2016. Resultados: Foram classificados 77 neonatos recém‐nascidos com risco de infecção fúngica invasiva, com base na hemocultura, em: grupo sem fungemia, incluindo 41 neonatos com sepse bacteriana comprovada, grupo com suspeita de fungemia, incluindo 25 neonatos com hemocultura negativa; e grupo com fungemia definida, incluiu 11 neonatos com Candida comprovada por cultura. Os organismos em crescimento foram: {Klebsiella spp 14/54; E. coli 12/54; Staphylococcus spp 12/54 (Staph coagulase negativa 9/54; Staph aureus 3/54); pseudomonous aerouginosa 3/54 e Proteus spp 2/54}, além de 11/54 Candida. A concentração de (1,3)‐β‐D‐glucano no soro foi significativamente inferior no grupo sem fungemia em comparação ao grupo com fungemia definida. O melhor valor de corte da (1,3)‐β‐D‐glucano foi 99 pg/mL com sensibilidade, especificidade, valor preditivo positivo, valor preditivo negativo e precisão de 63,6%, 95,1%, 77,8%, 90,7% e 88,5%, respectivamente. Conclusão: O ensaio de (1,3)‐β‐D‐glucano possui sensibilidade limitada com especificidade e valor preditivo negativo excelentes que possibilitam seu uso e ajudam na exclusão de infecção fúngica invasiva neonatal. O diagnóstico preciso e as decisões terapêuticas devem ter como base a combinação de ensaio de (1,3)‐β‐D‐glucano com outros achados clínicos, radiológicos e microbiológicos. Keywords: (1,3)‐β‐d‐glucan, Invasive candidiasis, Neonatal sepsis, Palavras‐chave: (1,3)‐β‐D‐glucano, Candidíase invasiva, Sepse neonata

Role of serum (1,3)-β-d-glucan assay in early diagnosis of invasive fungal infections in a neonatal intensive care unit

Objectives: To study the microbiological pattern of late onset neonatal sepsis cultures and to assess the diagnostic performance of serum (1,3)-β-d-glucan level for early diagnosis of invasive fungemia in high-risk infants admitted to a neonatal intensive care unit. Methods: A prospective multicenter clinical trial conducted on infants at high risk for invasive fungal infections, with suspected late onset sepsis, admitted to a neonatal intensive care unit at Mansoura University Children's Hospital and Mansoura General Hospital between March 2014 and February 2016. Results: A total of 77 newborn infants with high risk of invasive fungal infection were classified based on blood culture into three groups: no fungemia (41 neonates with proven bacterial sepsis), suspected fungemia (25 neonates with negative blood culture), and definite fungemia group (11 neonates with culture-proven Candida). The growing organisms were Klebsiella spp. (14/54); Escherichia coli (12/54); Staphylococcus spp. (12/54; coagulase-negative Staphylococcus [9/54]; Staphylococcus aureus [3/54]); Pseudomonas aerouginosa (3/54); and Proteus spp. (2/54). Moreover, 11/54 presented Candida. Serum (1,3)-β-d-glucan concentration was significantly lower in the no fungemia group when compared with the definite fungemia group. The best cut-off value of (1,3)-β-d-glucan was 99 pg/mL with sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 63.6%, 95.1%, 77.8%, 90.7%, and 88.5%, respectively. Conclusion: (1,3)-β-d-glucan assay has a limited sensitivity with excellent specificity and negative predictive value, which allow its use as an aid in exclusion of invasive neonatal fungal infection. Accurate diagnosis and therapeutic decisions should be based on combining (1,3)-β-d-glucan assay with other clinical, radiological, and microbiological findings. Resumo: Objetivos: Estudar o padrão microbiológico das culturas de sepse neonatal de início tardio e avaliar o desempenho diagnóstico do nível de (1,3)-β-D-glucano no soro para diagnóstico precoce de fungemia invasiva em neonatos de alto risco internados em uma unidade de terapia intensiva neonatal. Métodos: Ensaio clínico multicêntrico prospectivo conduzido em neonatos internados em uma unidade de terapia intensiva neonatal com suspeita de sepse de início tardio que estavam em risco de infecções fúngicas invasivas no hospital universitário infantil de Almançora e no hospital geral de Almançora entre março de 2014 e fevereiro de 2016. Resultados: Foram classificados 77 neonatos recém-nascidos com risco de infecção fúngica invasiva, com base na hemocultura, em: grupo sem fungemia, incluindo 41 neonatos com sepse bacteriana comprovada, grupo com suspeita de fungemia, incluindo 25 neonatos com hemocultura negativa; e grupo com fungemia definida, incluindo 11 neonatos com Candida comprovada por cultura. Os organismos em crescimento foram: {Klebsiella spp 14/54; E. coli 12/54; Staphylococcus spp 12/54 (Staph coagulase negativa 9/54; Staph aureus 3/54); pseudomonous aerouginosa 3/54 e Proteus spp 2/54}, além de 11/54 Candida. A concentração de (1,3)-β-D-glucano no soro foi significativamente inferior no grupo sem fungemia em comparação ao grupo com fungemia definida. O melhor valor de corte da (1,3)-β-D-glucano foi 99 pg/mL com sensibilidade, especificidade, valor preditivo positivo, valor preditivo negativo e precisão de 63,6%, 95,1%, 77,8%, 90,7% e 88,5%, respectivamente. Conclusão: O ensaio de (1,3)-β-D-glucano possui sensibilidade limitada com especificidade e valor preditivo negativo excelentes que possibilitam seu uso e ajudam na exclusão de infecção fúngica invasiva neonatal. O diagnóstico preciso e as decisões oterapêuticas devem ter como base a combinação di ensaio de (1,3)-β-D-glucano com outros achados clínicos, radiológicos e microbiológicos. Keywords: (1,3)-β-d-glucan, Invasive candidiasis, Neonatal sepsis, Palavras-chave: (1,3)-β-D-glucano, Candidíase invasiva, Sepse neonata