Catheter-associated urinary tract infections in Africa: Systematic review and meta-analysis
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References 27 publications
Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis
Background A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs. Methods A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity. Results A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72–4.81, p < 0.001, I 2 = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86–0.91, I 2 = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51–0.90, I 2 = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86–0.92). The GRADE score indicated a low CoE. Conclusion The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-024-09914-9.
Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis
Background A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs. Methods A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity. Results A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72–4.81, p < 0.001, I 2 = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86–0.91, I 2 = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51–0.90, I 2 = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86–0.92). The GRADE score indicated a low CoE. Conclusion The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-024-09914-9.
Progress on implementing the WHO-GLASS recommendations on priority pathogen-antibiotic sensitivity testing in Africa: A scoping review
Introduction The World Health Organization global antimicrobial resistance surveillance system (GLASS) was rolled out in 2015 to guide antimicrobial resistance (AMR) surveillance. However, its implementation in Africa has not been fully evaluated. We conducted a scoping review to establish the progress of implementing the WHO 2015 GLASS manual in Africa. Methods We used MeSH terms to comprehensively search electronic databases (MEDLINE and Embase) for articles from Africa published in English between January 2016 and December 2023. The Arksey and O'Malley's methodological framework for scoping reviews was employed. Data were collected on compliance with WHO GLASS recommendations for AMR surveillance-priority samples, pathogens, and pathogen-antibiotic combinations and analysed using Microsoft Excel. Results Overall, 13,185 articles were identified. 7,409 were duplicates, and 5,141 articles were excluded based on titles and abstracts. 609 full-text articles were reviewed, and 147 were selected for data extraction. Of the 147 selected articles, 78.9% had been published between 2020 and 2023; 57.8% were from Eastern Africa. 93.9% of articles were on cross-sectional studies. 96.6% included only one priority sample type; blood (n=56), urine (n=64), and stool (n=22). Of the 60 articles that focused on blood as a priority sample type, 71.7%, 68.3%, 68.3%, 36.7%, 30%, and 10% reported recovery of Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Salmonella species and Streptococcus pneumoniae, respectively. Salmonella and Shigella species were reported to have been recovered from 91.3% and 73.9% of the 23 articles that focused on stool. E. coli and K. pneumoniae recoveries were also reported from 94.2% and 68.1% of the 69 articles that focused on urine. No article in this review reported having tested all the recommended WHO GLASS pathogen-antibiotic combinations for specific pathogens. Conclusion Progress has been made in implementing the GLASS recommendations in Africa, but adoption varies across countries limiting standardisation and comparability of data.
Utility of syndromic surveillance for the surveillance of healthcare-associated infections in resource-limited settings: a narrative review
Globally, Healthcare-associated infections (HCAIs) pose a significant threat to patient safety and healthcare systems. In low- and middle-income countries (LMICs), the lack of adequate resources to manage HCAIs, as well as the weak healthcare system, further exacerbate the burden of these infections. Traditional surveillance methods that rely on laboratory tests are cost-intensive and impractical in these settings, leading to ineffective monitoring and delayed management of HCAIs. The rates of HCAIs in resource-limited settings have not been well established for most LMICs, despite their negative consequences. This is partly due to costs associated with surveillance systems. Syndromic surveillance, a part of active surveillance, focuses on clinical observations and symptoms rather than laboratory confirmation for HCAI detection. Its cost-effectiveness and efficiency make it a beneficial approach for monitoring HCAIs in LMICs. It provides for early warning capabilities, enabling timely identification and response to potential HCAI outbreaks. Syndromic surveillance is highly sensitive and this helps balance the challenge of low sensitivity of laboratory-based surveillance systems. If syndromic surveillance is used hand-in-hand with laboratory-based surveillance systems, it will greatly contribute to establishing the true burden of HAIs in resource-limited settings. Additionally, its flexibility allows for adaptation to different healthcare settings and integration into existing health information systems, facilitating data-driven decision-making and resource allocation. Such a system would augment the event-based surveillance system that is based on alerts and rumours for early detection of events of outbreak potential. If well streamlined and targeted, to monitor priority HCAIs such as surgical site infections, hospital-acquired pneumonia, diarrheal illnesses, the cost and burden of the effects from these infections could be reduced. This approach would offer early detection capabilities and could be expanded into nationwide HCAI surveillance networks with standardised data collection, healthcare worker training, real-time reporting mechanisms, stakeholder collaboration, and continuous monitoring and evaluation. Syndromic surveillance offers a promising strategy for combating HCAIs in LMICs. It provides early warning capabilities, conserves resources, and enhances patient safety. Effective implementation depends on strategic interventions, stakeholder collaboration, and ongoing monitoring and evaluation to ensure sustained effectiveness in HCAI detection and response.
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