Background: The burden of healthcare-associated infection (HAI) is 2 to 18 times higher in developing countries. However, few data are available regarding infection prevention and control (IPC) process indicators in these countries. We evaluated hand hygiene (HH) facilities and compliance amongst healthcare workers (HCW) in a 600-bed healthcare facility in Northcentral Nigeria providing tertiary care service for a catchment population of about 20 million. Methods: An in-house facility assessment tool and the World Health Organization (WHO) direct observation method were used to assess the HH facilities and compliance, respectively. Factors associated with good compliance were determined by multivariate analysis. Results: The facility survey was carried out in all 46 clinical units of the hospital. 72% of the units had no poster or written policy on HH; 87% did not have alcohol-based hand rubs; 98% had at least one handwash sink; 28% had flowing tap water all day while 72% utilized cup and bucket; and 58% had no hand drying facilities. A total of 406 HH opportunities were observed among 175 HCWs. The overall compliance was 31%, ranging from 18% among ward attendants to 82% among medical students. Based on WHO “5 moments” for HH, average compliance was 21% before patient contact, 23% before aseptic procedure, 63% after body fluid exposure risk, 41% after patient contact and 40% after contact with patients’ surrounding. Being a medical student was independently associated with high HH compliance, adjusted odds ratio: 13.87 (1.70–112.88). Conclusions: Availability of HH facilities and HCW compliance in a large tertiary hospital in Nigeria is poor. Our findings confirm that HCWs seem more sensitized to their risk of exposure to potential pathogens than to the prevention of HAI cross-transmission. Inadequate HH facilities probably contributed to the poor compliance. Specific measures such as improved facilities, training and monitoring are needed to improve HH compliance.

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.

R and surface contamination in the special care baby unit of a tertiary hospital in Jos, Nigeria. METHODS Surface and air samples were cultured and antibiotic susceptibility of isolated bacteria were determined. RESULTS The bacterial profile of air and surface samples showed that Klebsiella was the most common bacteria followed by Staphyllococcus; while the least was Escherichia. Most of the bacteria were isolated from the out-born term area of the special care baby unit. All the bacteria isolated were susceptible to ceftriaxone and meropenem. CONCLUSION This study showed that all areas of the special care baby unit of the hospital have bacterial, indicating that these are a potential source of cross-infection from healthcare workers to the neonatal patients. Correspondence: Mark O. Okolo Department of Medical Microbiology, Jos University Teaching Hospital, Jos, Nigeria. E-mail:okolomark@gmail.com This is an open access journal, and articles are distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as appropriate credit is given and the new creations are licensed under the identical terms. © 2016 Nigerian Journal of Medicine | Published by Wolters Kluwer – Medknow...

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.

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.