Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
Background Evaluation of antimicrobial susceptibility profile of various bacterial pathogens in the health facilities, abattoirs and related environment is important to assess potential risk of dissemination of resistant pathogens to the environment. There is limited information about antimicrobial susceptibility profile of common Enterobacteriaceae in waste water samples from hospitals, abattoirs and the downstream water bodies in Addis Ababa. The present study assessed antimicrobial susceptibility of bacteria belonging to the family Enterobacteriaceae isolated from wastewater samples (WWS) of two hospitals: Tikur Anbessa Specialized Hospital (TASH) and Minilik II hospital, a wastewater treatment plant (WWTP) and an abattoir, and downstream rivers in Addis Ababa. Results A total of 54 bacterial isolates belonging to 6 species were identified: E.coli (32%), Salmonella 23%), Klebsiella pneumonia (15%), Enterobacter aerogenes (11%), Citrobacter (7%), Klebsiella oxytoca (6%) and Enterobacter cloacae (6%), respectively. Two strains of Citrobacter spp. isolated from TASH wastewater sample (WWS) were resistant to all 12 antimicrobials tested whereas an E. coli isolate from the same source was resistant to 11 antimicrobials. All isolates were resistant to 2 or more antimicrobials tested. Multi-drug resistance (MDR) to several antimicrobials was recorded, particularly in isolates obtained from hospital WWS and it was more common in Citrobacter and E. coli isolates. Extended spectrum betalactamase (ESBL) production was detected in 27.3% of MDR isolates, all of them obtained from hospital effluents whereas none of the isolates were carbapenemase producers. Conclusion The present study revealed that Enterobacteriaceae in wastewater from hospitals, abattoir and downstream water bodies are resistant to commonly used antimicrobials. Hospital effluents contained more of MDR bacteria, posing significant public health threat through dissemination to the downstream water bodies.
Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.
Background COVID-19 is an ongoing public health pandemic regardless of the countless efforts made by various actors. Quality diagnostic tests are important for early detection and control. Notably, several commercially available one step RT-PCR based assays have been recommended by the WHO. Yet, their analytic and diagnostic performances have not been well documented in resource-limited settings. Hence, this study aimed to evaluate the diagnostic sensitivities and specificities of three commercially available one step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in Ethiopia in clinical setting. Methods A cross-sectional study was conducted from April to June, 2021 on 279 respiratory swabs originating from community surveillance, contact cases and suspect cases. RNA was extracted using manual extraction method. Master-mix preparation, amplification and result interpretation was done as per the respective manufacturer. Agreements between RT-PCRs were analyzed using kappa values. Bayesian latent class models (BLCM) were fitted to obtain reliable estimates of diagnostic sensitivities, specificities of the three assays and prevalence in the absence of a true gold standard. Results Among the 279 respiratory samples, 50(18%), 59(21.2%), and 69(24.7%) were tested positive by TIB, Da An, and BGI assays, respectively. Moderate to substantial level of agreement was reported among the three assays with kappa value between 0 .55 and 0.72. Based on the BLCM relatively high specificities (95% CI) of 0.991(0.973–1.000), 0.961(0.930–0.991) and 0.916(0.875–0.952) and considerably lower sensitivities with 0.813(0.658–0.938), 0.836(0.712–0.940) and 0.810(0.687–0.920) for TIB MOLBIOL, Da An and BGI respectively were found. Conclusions While all the three RT-PCR assays displayed comparable sensitivities, the specificities of TIB MOLBIOL and Da An were considerably higher than BGI. These results help adjust the apparent prevalence determined by the three RT-PCRs and thus support public health decisions in resource limited settings and consider alternatives as per their prioritization matrix.
Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Despite cultivation-based methods routinely employed in monitoring drinking water quality, cultivation of speci c indicator organisms alone is not always guarantee for assuring safe drinking water delivery. The presence of complex microbiomes in drinking water distribution systems affects treatment effectiveness leading to poor quality water which as a result affects health of human and animals. Drinking water treatment and distribution systems harbor various microbiota despite efforts made in improving water infrastructures and several waterborne diseases become serious problems in the water industry, specially, in developing Countries. Intermittent water supply, long-time of water storage, low water pressure in distribution systems, storage tankers and pipes as well as contaminated source water are among many of the factors responsible for low drinking water quality which in turn affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and several household points of use locations (taps). High throughput Illumina sequencing technology was employed by targeting V4 region of 16S rRNA following Illumina protocol to analyze the community structure of bacteria. The core dominating taxa were Proteobacteria followed by Firmicutes, Bacteroidetes and Actinobacteria. Gamma proteobacteria were dominant among other Proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmanella, Acanthamoeba, Aspergillus, and Candida were also the abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations were in uenced by factors such as residual free chlorine, intermittent water supply and long-time storage at the household. The shift in microbial community structure from source to point of use locations were in uenced by factors such as residual free chlorine, intermittent water supply and long-time storage at the household. The complex microbiota which was present in different sample sites receiving treated water from the two treatment plants (Legedadi and Gefersa) starting from source water to household point of consumption across the distribution systems in Addis Ababa brings drinking water quality problem which further causes signi cant health problems to both human and animal health. Treatment ineffectiveness, disinfection ine ciency, poor maintenance actions, leakage of sewage and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk which, this, leads to morbidity and mortality. Findings of this research provide important and bassline information to understand th...
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