Background. Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to (1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, (2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa and (3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods. This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English language studies published from 1 January 2008 to 30 April 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL and the Cochrane Library. The protocol was publicly available on the Open Science Framework Bastug et al. (Nanopore Sequencing for Infectious Diseases Surveillance and Diagnostics in Africa: a Scoping Review 2024) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results. One thousand one hundred sixty-two studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analysed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African country and 11% in a non-African country, while 32% did not specify the location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious disease outbreak, 25 of which studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline, and five studies published the per-specimen cost. Conclusions. ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Most studies used ONT for genomic surveillance of pathogens or antimicrobial resistance genes, while only one study used ONT directly for a real-time clinical application. A small number of studies described a short interval between specimen collection and sequence result, supporting that clinical applications are possible. There is a need for improved reporting of ONT methodology including pipeline timelines, cost, use of barcoding, flow cell models and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low-resource settings.

Escherichia coli is a gram-negative commensal bacterium living in human and animal intestines. Its pathogenic strains lead to high morbidity and mortality, which can adversely affect people by causing urinary tract infections, food poisoning, septic shock, or meningitis. Humans can contract E. coli by eating contaminated food—such as raw or undercooked raw milk, meat products, and fresh produce sold in open markets—as well as by coming into contact with contaminated settings like wastewater, municipal water, soil, and faeces. Some pathogenic strains identified in Nigeria, include Enterohemorrhagic (Verotoxigenic), Enterotoxigenic, Enteropathogenic, Enteroinvasive, and Enteroaggregative E. coli. This causes acute watery or bloody diarrhoea, stomach cramps, and vomiting. Apart from the virulence profile of E. coli, antibiotic resistance mechanisms such as the presence of bla_CTX-M found in humans, animals, and environmental isolates are of great importance and require surveillance and monitoring for emerging threats in resource-limited countries. This review is aimed at understanding the underlying mechanisms of evolution and antibiotic resistance in E. coli in Nigeria and highlights the use of improving One Health approaches to combat the problem of emerging infectious diseases.

Presently, the global public health threat of international concern is the coronavirus disease-2019 (COVID-19), a viral disease of worldwide prevalence caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), at present the disease has no known cure or vaccine. Plants worldwide including plants of African ethnopharmacological relevance are a natural source of abundant and diverse phytochemicals with bioactivity against microorganisms including viruses. We selected 13 plants used in African traditional medicine for the treatment of viral diseases to screen for phytochemicals capable of interfering with SARS-CoV-2 therapeutic targets using AutoDock Vina in silico tool. 25 phytochemicals from these plants that passed the Lipinski rule of drug-likeness were assessed for antiviral activity against three SARS-CoV-2 therapeutic targets, namely: spike glycoprotein, Papain-like protease and 3C-like proteinase. The crystal structure of the viral protein targets was obtained from the protein databank website (https://www.rcsb.org/). The active sites of the target proteins were predicted using SCFBio Server (http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp) from the PDB file as input. The antiviral herbal phytochemical compounds were then docked with prepared targets: Papain-like protease, 3C-like proteinase and spike glycoprotein. The Autodocking hit results generated six lead phytochemicals out of a library of twenty-five (25) phytochemicals from the African traditional herbs with potential anti-SARS-CoV-2 activity. The lead molecules with their binding affinities against Papain-like protease and 3C-Like Proteinase are as follows: Ginsenosides (-9.9 kcal/mol), ursolic acid (-9.4 kcal/mol), oleanolic acid (-9.4 kcal/mol), cynarine (-8.9 kcal/mol), glabridin (-8.5 kcal/mol) and cinnamoyl-echinadiol (-8.2 kcal/mol). ADMET profile shows glabridin, cinnamoyl-echinadiol and neral obtained from Licorice, Echinacea purpurea and lemongrass respectively, exhibited best-fit values as drugs candidate. We advocate for further in vitro and in vivo studies to evaluate the activity of these lead compounds with a view to optimized drug intervention against COVID-19 pandemic.

Background: Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective, and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to: 1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, 2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa, and 3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods: This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English‐language studies published from January 1, 2008, to April 30, 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL, and the Cochrane Library. The protocol was publicly available on the Open Science Framework (1) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results: 1162 studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analyzed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African Country, 11% in a non-African country, and 32% did not specify location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum, or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious diseases outbreak, 25 of which studied SARS-CoV-2. Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle, and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline and five studies published the per-specimen cost. Conclusions: ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Improved reporting of ONT-specific methodology is needed, including timelines, cost, barcoding, flow cell model, and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low resource settings.

Escherichia coli is a gram-negative commensal bacterium living in human and animal intestines. Its pathogenic strains are cause of high morbidity which can adversely affect people by causing urinary tract infections, food poisoning, septic shock, or meningitis. Humans can contract E. coli by eating contaminated food—such as raw or undercooked raw milk, meat products, and fresh produce sold in open markets—as well as by coming into contact with contaminated settings like wastewater, municipal water, soil, and faeces. Some pathogenic strains of E. coli have been identified in Nigeria such as enterohemorrhagic (EHEC), as well as enterotoxigenic (ETEC), enteropathogenic (EPEC), enteroinvasive (EIEC), enteroaggregative (EAEC), and verotoxigenic (VTEC). This causes acute watery or bloody diarrhoea, stomach cramps, and vomiting. Apart from the virulence profile of E. coli, antibiotic resistance mechanisms such as the presence of blaCTX-M found in humans, animals and environmental isolates which are of great importance and require surveillance and monitoring for emerging threats in resource-limited countries. This review is aimed at understanding the underlying mechanisms of evolution and antibiotic resistance in E. coli in Nigeria and highlighting the use of improving One Health approaches to combat the problem of emerging infectious diseases.

Background:Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective, and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to: 1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, 2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa, and 3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods: This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English‐language studies published from January 1, 2008, to April 30, 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL, and the Cochrane Library. The protocol was publicly available on the Open Science Framework (1) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results: 1162 studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analyzed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African Country, 11% in a non-African country, and 32% did not specify location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum, or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious diseases outbreak, 25 of which studied SARS-CoV-2. Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle, and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline and five studies published the per-specimen cost. Conclusions: ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Most studies used ONT for genomic surveillance of pathogens or antimicrobial resistance genes, while only one study used ONT directly for a real-time clinical application. A small number of studies described a short interval between specimen collection and sequence result, supporting that clinical applications are possible. There is a need for improved reporting of ONT methodology including pipeline timelines, cost, use of barcoding, flow cell models, and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low resource settings.