Pathways of exposure to Vibrio Cholerae in an urban informal settlement in Nairobi, Kenya.

Cholera is a diarrhoeal disease caused by Vibrio cholerae (V. cholerae) bacterium, with strains belonging to serogroups 01 and 0139 causing a huge proportion of the disease. V. cholerae can contaminate drinking water sources and food through poor sanitation and hygiene. This study aimed to identify environmental routes of exposure to V. cholerae within Mukuru informal settlement in Nairobi. We collected nine types of environmental samples (drinking water, flood water, open drains, surface water, shaved ice, raw produce, street food, soil, and public latrine swabs) over 12 months. All samples were analysed for V. cholerae by culture and qPCR, then qPCR-positive samples were quantified using a V. cholerae DNA standard. Data about the frequency of contact with the environment was collected using behavioural surveys. Of the 803 samples collected, 28.5% were positive for V. cholerae by qPCR. However, none were positive for V. cholerae by culture. V. cholerae genes were detected in majority of the environmental water samples (79.3%), including open drains, flood water, and surface water, but were only detected in small proportions of other sample types. Vibrio-positive environmental water samples had higher mean V. cholerae concentrations [2490-3469 genome copies (gc) per millilitre (mL)] compared to drinking water samples (25.6 gc/mL). Combined with the behavioural data, exposure assessment showed that contact with surface water had the highest contribution to the total V. cholerae exposure among children while ingestion of municipal drinking water and street food and contact with surface water made substantial contributions to the total V. cholerae exposure for adults. Detection of V. cholerae in street food and drinking water indicates possible risk of exposure to toxigenic V. cholerae in this community. Exposure to V. cholerae through multiple pathways highlights the need to improve water and sanitation infrastructure, strengthen food hygiene practices, and roll out cholera vaccination.

Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?

Introduction: Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions. Methods: We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA. Results and Discussion: The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings. Conclusion: A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.

Application of Adaptive Evolution to Improve the Stability of Bacteriophages during Storage.

Phage stability is important for the successful application of bacteriophages as alternative antibacterial agents. Considering that temperature is a critical factor in phage stability, this study aimed to explore the possibility of improving long-term phage stability through adaptive evolution to elevated temperature. Evolution of three wild-type ancestral phages (Myoviridae phage Wc4 and Podoviridae phages CX5 and P-PSG-11) was induced by subjecting the phages to heat treatment at 60 °C for five cycles. The adapted phages showed better stability than the wild-type ancestral phages when subjected to heat treatment at 60 °C for 1 h and after 60 days of storage at 37 °C. However, the adapted phages could not withstand thermal treatment at 70 °C for 1 h. The infectivity and the lytic properties of the phages were not changed by the evolution process. Whole-genome sequencing revealed that single substitutions in the tail tubular proteins were the only changes observed in the genomes of the adapted phages. This study demonstrates that adaptive evolution could be used as a general method for enhancing the thermal stability of phages without affecting their lytic activity. Sequencing results showed that bacteriophages may exist as a population with minor heterogeneous mutants, which might be important to understand the ecology of phages in different environments.

Molecular Detection and Genetic Characterization of Novel RNA Viruses in Wild and Synanthropic Rodents and Shrews in Kenya.

The majority of emerging and reemerging zoonotic viral pathogens are RNA viruses. Pathogen discovery programs of emerging infectious diseases (EIDs) in wildlife have implicated rodents and shrews as hosts of diverse human pathogens, such as hantaviruses, arenaviruses, paramyxoviruses, etc. Despite these threats, little is known about the diversity of viruses circulating among rodents and shrews in Kenya, meaning the risk of infectious disease outbreak from these small mammals could be oblivious. This study reports the first surveillance toward understanding the diversity of RNA viruses carried by rodents and shrews in areas of high-potential contact with humans in Kenya through molecular detection. A total of 617 samples comprising fecal, urine, and tissues from 138 rodents and 5 shrews were screened for eight different families of viruses using RT-PCR assays. The results highlight the presence of diverse astroviruses, paramyxoviruses, hepeviruses, and arenavirus, circulating in both wild and synanthropic Kenyan rodents and shrews. Most of the viruses detected in this study are novel strains and some belong to the families that contain important human viral pathogens. Notably, a novel arenavirus was detected in Grammomys macmillani, a rodent species newly identified to harbor arenavirus, and it potentially represent a novel arenavirus species. Our findings demonstrate the need for continued pathogen surveillance among these small mammals as well as among the vulnerable and exposed livestock and humans. This would help in development and implementation of effective preventive and control strategies on EIDs in countries with rich wildlife biodiversity like Kenya.

Droplet digital PCR applications in the tuberculosis world.

Droplet digital polymerase chain reaction (ddPCR) is a third generation of polymerase chain reaction (PCR) that enables the exact quantification of nucleic acid targets within a sample. The capability of ddPCR to accurately detect and quantify low abundant targets has led to its fast-growing applications in detection of different pathogens. This review summarizes the ddPCR technology and its applications in tuberculosis diagnosis. From current studies including a total of 9 publications on the applications of ddPCR in tuberculosis research, it is clear that ddPCR technology offers enormous advantages, such as unparalleled sensitivity, high precision, and absolute quantification without a standard curve, over common molecular diagnostic platforms like the real-time quantification PCR. The latest study also showed that rapid drug susceptibility test of Mycobacterium tuberculosis in sputa could be achieved within 4 days. However, the high cost is the main limitation for its wide applications, especially in developing countries. As we near the vision 2030 goal for sustainable development and ending the tuberculosis epidemic by 2030, ddPCR techniques may help achieve this objective and many more discussed in the UNGA-HLM-TB.

Biocontrol of phytobacteria with bacteriophage cocktails.

Crop loss due to plant pathogens has provoked renewed interest in bacteriophages as a feasible biocontrol strategy of plant diseases. Phage cocktails in particular present a viable option for broadening the phage host range, limiting the emergence of bacterial resistance while maintaining the lytic activity of the phages. It is therefore important that the design used to formulate a phage cocktail should result in the most effective cocktail against the pathogen. It is also critical that certain factors are considered during the formulation and application of a phage cocktail: their stability, the production time and cost of complex cocktails, the potential impact on untargeted bacteria, the timing of phage application, and the persistence in the plant environment. Continuous monitoring is required to ensure that the efficacy of a cocktail is sustained due to the dynamic nature of phages. Although phage cocktails are considered as a plausible biocontrol strategy of phytobacteria, more research needs to be done to understand the complex interaction between phages and bacteria in the plant environment, and to overcome the technical obstacles. © 2019 Society of Chemical Industry.