RESUMO
Pseudomonas aeruginosa is a leading cause of nosocomial infections worldwide. It can produce a range of debilitating infections, have a propensity for developing antimicrobial resistance, and present with a variety of potent virulence factors. This study investigated the sequence types (ST), phenotypic antimicrobial susceptibility profiles, and resistance and virulence genes among clinical isolates from urinary tract and skin and soft tissue infections. Fifty-six P. aeruginosa clinical isolates were obtained from six medical centers across five counties in Kenya between 2015 and 2020. Whole-genome sequencing (WGS) was performed to conduct genomic characterization, sequence typing, and phylogenetic analysis of the isolates. Results showed the presence of globally distributed high-risk clones (ST244 and ST357), local high-risk clones (ST2025, ST455, and ST233), and a novel multidrug-resistant (MDR) clone carrying virulence genes (ST3674). Furthermore, 31% of the study isolates were found to be MDR with phenotypic resistance to a variety of antibiotics, including piperacillin (79%), ticarcillin-clavulanic acid (57%), meropenem (34%), levofloxacin (70%), and cefepime (32%). Several resistance genes were identified, including carbapenemases VIM-6 (ST1203) and NDM-1 (ST357), fluoroquinolone genes, crpP, and qnrVCi, while 14 and 22 different chromosomal mutations were detected in the gyrA and parC genes, respectively. All isolates contained at least three virulence genes. Among the virulence genes identified, phzB1 was the most abundant (50/56, 89%). About 21% (12/56) of the isolates had the exoU+/exoS- genotype, while 73% (41/56) of the isolates had the exoS+/exoU- genotype. This study also discovered 12 novel lineages of P. aeruginosa, of which one (ST3674) demonstrated both extensive antimicrobial resistance and the highest number of virulence genes (236/242, 98%). Although most high-risk clones were detected in Nairobi County, high-risk and clones of interest were found throughout the country, indicating the local spread of global epidemic clones and the emergence of new strains. Thus, this study illustrates the urgent need for coordinated local, regional, and international antimicrobial resistance surveillance efforts.
RESUMO
According to the United Nations Educational, Scientific, and Cultural Organization (UNESCO), Open Science is the movement to make scientific research and data accessible to all. It has great potential for advancing science. At its core, it includes (but is not limited to) open access, open data, and open research. Some of the associated advantages are promoting collaboration, sharing and reproducibility in research, and preventing the reinvention of the wheel, thus saving resources. As research becomes more globalized and its output grows exponentially, especially in data, the need for open scientific research practices is more evident - the future of modern science. This has resulted in a concerted global interest in open science uptake. Even so, barriers still exist. The formal training curriculum in most, if not all, universities in Kenya does not equip students with the knowledge and tools to subsequently practice open science in their research. Therefore, to work openly and collaboratively, there is a need for awareness and training in the use of open science tools. These have been neglected, especially in most developing countries, and remain barriers to the cause. Moreover, there is scanty research on the state of affairs regarding the practice and/or adoption of open science. Thus, we developed, through the OpenScienceKE framework, a model to narrow the gap. A sensitize-train-hack-collaborate model was applied in Nairobi, the economic and administrative capital of Kenya. Using the model, we sensitized through seminars, trained on the use of tools through workshops, applied the skills learned in training through hackathons to collaboratively answer the question on the state of open science in Kenya. While the former parts of the model had 20-50 participants, the latter part mainly involved participants with a bioinformatics background, leveraging their advanced computational skills. This model resulted in an open resource that researchers can use to publish as open access cost-effectively. Moreover, we observed a growing interest in open science practices in Kenya through literature search and data mining and that lack of awareness and skills may still hinder the adoption and practice of open science. Furthermore, at the time of the analyses, we surprisingly found that out of the 20,069 papers downloaded from BioRXiv, only 18 had Kenyan authors, a majority of which are international (16) collaborations. This may suggest poor uptake of the use of preprints among Kenyan researchers. The findings in this study highlight the state of open science in Kenya and challenges facing its adoption and practice while bringing forth possible areas for primary consideration in the campaign toward open science. It also proposes a model (sensitize-train-hack-collaborate model) that may be adopted by researchers, funders and other proponents of open science to address some of the challenges faced in promoting its adoption in Kenya.
