Susceptibility of mycotoxigenic fungi to commercial fungicides, a potential tool for mycotoxin control in maize in Kenya

Mycotoxin contamination of food grains represents significant health and economic challenges in developing countries as well as the developed world. Mycotoxin- producing fungal species affecting maize mainly belong to the genera Aspergillus, Fusarium, and Penicillium.They pose serious phytopathological and mycotoxicological risks both at pre-harvest and post-harvest stages. Maize in Kenya has been associated with frequent outbreaks of aflatoxin contamination. A number of mycotoxin control strategies both chemical and biological have been developed as potential tools for mycotoxin control. A Laboratory based cross-sectional study was carried out in a Mycology Laboratory at the Center for Microbiology Research in Kenya Medical Research Institute, Nairobi, Kenya. A total of 138 maize samples obtained from Machakos, Nairobi, Mombasa, Kitale and Kisumu were subjected to mycological analysis. The samples were treated with the fungicides; Antracol (propineb), Milraz (propineb700g/kg and Cymoxanil60g/kg), Mistress (Cymoxanil 8% and Mancozeb 64%) and Victory (Metalaxy 80g/kg and Mancozeb 640g/kg.) before inoculation on Sabourauds dextrose agar (SDA). Infestation rates on fungicide- treated and non treated control maize kernels were scored. The susceptibility of the isolates to the four test fungicides was determined by disk diffusion technique. All the maize samples were infested by moulds and there was a significant difference in regional infestation rates (p<0.05). Maize from Mombasa had the lowest infestation of 72.5% while Nairobi was the highest with 99.1%. Fungi of the genera Aspergillus, Fusarium, and Penicillium were frequently isolated from the five regions. There was a significant reduction {p<0.05 (0.00)} of infestation rates on fungicide- treated maize compared to the untreated. Generally, 26% (n=35) and 34% (n=47) of maize samples treated with Mistress and Victory, respectively had 0% infestation while those treated with Milraz and Antracol were 10% (n=14) and 14% (n=19), respectively. Some mycotoxigenic isolates were found to be resistant to more than one of the test fungicides. However, their in- vitro antifungal activity is of great importance and could further be evaluated to determine their field efficacy for mycotoxin control in maize.Key words: Maize, Mycotoxigenic fungi, Fungicides, Susceptibility

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Characterization of Methicillin-Resistant Staphylococcus Aureus from Skin and Soft Tissue Infections in Patients in Nairobi, Kenya

Article JournalSkin and soft tissue infections (SSTIs) are among the most common infectious diseases and a frequent cause of hospital visits. In this study we sought to assess the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and antibiotic susceptibility patterns in SSTIs in patients attending hospitals in Kenya. Methods: Eighty-two S. aureus isolates recovered from SSTIs from both inpatients and outpatients were screened for antibiotic susceptibility, possession of staphylococcal cassette chromosome mec (SCCmec)gene type, and the Panton–Valentine leukocidin (PVL) toxin gene. The prevalence of MRSA was investigated in relation to the type of patient and infection type, as well as the type of health care facility. Results: Of 60 boil cultures, 39 (65%) grew S. aureus, of out of which 34 (87.2%) were MRSA. Of the 60 abscess cultures, 14 (23.3%) grew S. aureus, of which 10 (71.4%) were MRSA. Of 34 cellulitis cultures, 18 (52.9%) grew S. aureus, of which 16 (88.8%) were MRSA. Of 25 ulcer cultures, 11 (44%) grew S. aureus, of which nine (81.8%) were MRSA. Sixty-nine of 82 S. aureus (84.1%) were MRSA, with 52 (75.4%) possessing SCCmec II type and 14 (20.3%) being positive for the PVL gene. Based on hospitals, it was noted that most MRSA were isolated at publicly funded health care facilities serving an economically disadvantaged segment of Nairobi’s population, such as those living in urban informal settlements. All 82 S. aureus were susceptible to vancomycin and resistant in high numbers to macrolides, aminoglycosides, and quinolones. Bacterial isolates were mostly susceptible to vancomycin, ciprofloxacin and co-trimoxazole, and none was resistant to vancomycin. However, most organisms showed decreased susceptibility to erythromycin and clindamycin. Conclusions: These findings suggest that SCCmec II MRSA and a PVL strain of MRSA are significant pathogens in patients with SSTIs presenting to hospitals in Kenya, and that MRSA cases are prevalent at publicly funded health care facilities

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention