4 research outputs found
“Projecting the effects of non-pharmaceutical interventions and vaccination on COVID-19 control in Lusaka using a mathematical model”.
No full textThesis of Master’s of Science degree in One Health Analytical Epidemiology.The COVID-19 epidemic in Zambia has had significant social and economic impact on the health sector and wellbeing of the population. Hence it is vital to investigate the effect of various Interventions that were implemented to control the spread of the pandemic. Non-pharmaceutical
interventions (NPIs) were introduced to help contain the spread of COVID- 19 pandemic in the absence of pharmaceutical interventions. Since then, COVID-19 vaccines have been developed and are readily available globally. Projecting the combined impact of vaccine uptake and NPIs in the control of the COVID 19 pandemic is crucial to support evidence-based policy making. The Vensim Personal Learning Edition (PLE) simulation software was used to create a modified Susceptible-Exposed-Infectious-Recovered (SEIR) mathematical model to show the simultaneous effects of vaccination combined with NPIs such as social distance, hand hygiene and cough etiquette which we termed as behaviour change, and also vaccination with face
masking only against COVID-19 in Lusaka. Behaviour change and face masking were simulated at different percentages compliance together with varying vaccine uptake levels of low, moderate and high. Twelve different scenarios for groups of people who practice behaviour change or combined (NPIs) with vaccination and twelve scenarios for face masking with vaccination were modelled. Results from the simulation showed a reduction in the number of both cumulative cases and deaths from the interventions put in place as compared to scenarios without intervention. Furthermore, the basic reproduction number (R0) which was initially set at 2.64 in the model and was reduced to 2.37 in the scenario set at 10% behaviour change with low vaccination rate and 2.34 in the scenario set at 10% behaviour change with high vaccination rate as well as 0.61 in the scenario set at 80% behaviour change with low vaccination rate and 0.55 in the scenario set at 80% behaviour change with high vaccination rate. In the masking with vaccination scenarios, reproduction number was reduced to 2.45 in the scenario set at 10% masking with low vaccination rate and 2.29 in the scenario set at 10% masking with high vaccination rate as well as 1.25 in the scenario set at 80% masking with low vaccination rate and 1.24 in the scenario set at
80% masking with high vaccination rate. These findings highlight the importance of continued adherence to NPIs even when the population is being vaccinated, particularly under scenarios of lower vaccination rates which are influenced by vaccine efficacy, distribution and community hesitancy
Genomic characterization of cefotaxime-resistant Proteobacteria isolated from a bat-harboring cave in Zambia
No full textBats are widely recognized as reservoirs of emerging and re-emerging pathogens, and their ecological interactions with humans and livestock present important opportunities for the transmission of infectious agents and antimicrobial resistance (AMR). However, little is known about the occurrence of resistant bacteria in bat-associated environments in Zambia or their potential role in the maintenance of AMR outside clinical and agricultural settings. This study investigated the genomic characteristics of cefotaxime-resistant Proteobacteria isolated from bat fecal droppings collected at Leopards Hill Cave, an established hotspot for zoonotic pathogens. Four hundred bat fecal samples were cultured on cefotaxime-supplemented MacConkey agar, and those exhibiting bacterial growth were subjected to antimicrobial susceptibility testing and whole-genome analysis. Of the 400 samples processed, four (1 %) yielded growth, resulting in three bacterial species: Pseudomonas aeruginosa (n = 1), Enterobacter mori (n = 1), and Brucella intermedia (formerly Ochrobactrum intermedium) (n = 2). Genomic screening revealed that P. aeruginosa strain CB_234 harbored blaOXA-50, aph(3′)-IIb, and catB7, which confer resistance to β-lactams, aminoglycosides, and chloramphenicol, respectively. It also possessed multiple virulence determinants involved in adherence, motility, and secretion systems that enhance host colonization and environmental persistence. Core genome phylogenetic analysis placed CB_234 within a clade exclusively composed of clinical isolates from Nigeria, Thailand, Russia, Kenya, and Ghana, indicating a shared evolutionary lineage among globally dispersed hospital-associated strains. Conversely, environmental isolates from plant and aquatic sources, along with a dog-associated isolate, were phylogenetically distant, highlighting the distinct evolutionary origins. The E. mori isolate carried blaACT and qnrE resistance genes and plasmid replicons, suggesting potential mobility of resistance traits through horizontal gene transfer. In contrast, the two B. intermedia isolates did not harbor any known AMR genes or plasmid replicons. However, this species is increasingly recognized as an opportunistic pathogen. The detection of AMR-associated bacterial species in a natural bat habitat supports the evidence of resistance determinants circulating in wildlife environments in Zambia. Given that bats are unlikely to encounter clinical antibiotics directly, the persistence of such genes in their environment suggests that natural ecosystems may play an underappreciated role in maintaining AMR reservoirs independent of direct antimicrobial pressure. These findings underscore the importance of incorporating wildlife and environmental niches into national and global AMR surveillance frameworks under a One Health approach to better understand the ecological dimensions of AMR emergence and dissemination
In silico characterization of chromosomally integrated blaCTX-M genes among clinical Enterobacteriaceae in Africa: insights from whole-genome analysis
No full textAntimicrobial resistance (AMR) mediated by extended-spectrum β-lactamases (ESBLs) is a growing global concern, particularly among Enterobacteriaceae. The CTX-M-type ESBLs, encoded by the blaCTX-M gene, are of significant public health importance due to their high prevalence and broad geographic distribution. Typically located on plasmids and often co-occurring with other AMR genes, blaCTX-M contributes to multidrug resistance (MDR). However, increasing evidence suggests secondary chromosomal integration of blaCTX-M, sometimes alongside other resistance determinants. The extent and implications of this mechanism remain poorly characterized, especially in Africa, where genomic surveillance is limited. In this study, we retrieved 295 chromosomal sequences of Enterobacteriaceae of African origin from the GenBank and performed in silico predictions of blaCTX-M and other AMR genes. blaCTX-M-carrying sequences were further characterized by in silico multilocus sequence typing and genome annotation. Chromosomal insertions were identified through alignment with reference genomes. Overall, 47 of 295 sequences (15.9%) harbored the blaCTX-M gene, with the highest prevalence in Klebsiella pneumoniae (29/157, 18.5%), followed by Escherichia coli (13/72, 18.1%), Enterobacter spp. (4/38, 10.5%), and Shigella spp. (1/12, 8.3%). The most common allele was blaCTX-M-15 (31/47, 66.0%), followed by blaCTX-M-14 (12/47, 25.5%), blaCTX-M-55 (3/47, 6.4%), and blaCTX-M-27 (1/27, 3.7%). Co-occurrence of blaCTX-M with additional AMR genes was frequently observed, with integration events often associated with mobile genetic elements such as ISEcp1 and IS26. Notably, strains from the same hospital setting were phylogenetically related and shared sequence types and AMR gene profiles, suggesting local clonal dissemination. These findings reveal a notable presence of chromosomally integrated blaCTX-M among African Enterobacteriaceae, frequently in association with other resistance genes, thereby facilitating stable MDR propagation independent of plasmid maintenance. This evolutionary adaptation may have significant implications for the persistence and spread of MDR in clinical settings
Early Diagnosis of HIV Infection in Infants - One Caribbean and Six Sub-Saharan African Countries, 2011-2015.
No full textPediatric human immunodeficiency virus (HIV) infection remains an important public health issue in resource-limited settings. In 2015, 1.4 million children aged 50% decline. The most common challenges for access to testing for early infant diagnosis included difficulties in specimen transport, long turnaround time between specimen collection and receipt of results, and limitations in supply chain management. Further reductions in HIV mortality in children can be achieved through continued expansion and improvement of services for early infant diagnosis in PEPFAR-supported countries, including initiatives targeted to reach HIV-exposed infants, ensure access to programs for early infant diagnosis of HIV, and facilitate prompt linkage to treatment for children diagnosed with HIV infection
