The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

INTRODUCTION The global scale-up in demand for animal protein is the most notable dietary trend of our time. Since 2000, meat production has plateaued in high-income countries but has grown by 68%, 64%, and 40% in Asia, Africa, and South America, respectively. The transition to high-protein diets in low- and middle-income countries (LMICs) has been facilitated by the global expansion of intensive animal production systems in which antimicrobials are used routinely to maintain health and productivity. Globally, 73% of all antimicrobials sold on Earth are used in animals raised for food. A growing body of evidence has linked this practice with the rise of antimicrobial-resistant infections, not just in animals but also in humans. Beyond potentially serious consequences for public health, the reliance on antimicrobials to meet demand for animal protein is a likely threat to the sustainability of the livestock industry, and thus to the livelihood of farmers around the world. RATIONALE In LMICs, trends in antimicrobial resistance (AMR) in animals are poorly documented. In the absence of systematic surveillance systems, point prevalence surveys represent a largely untapped source of information to map trends in AMR in animals. We use geospatial models to produce global maps of AMR in LMICs and give policy-makers—or a future international panel—a baseline for monitoring AMR levels in animals and target interventions in the regions most affected by the rise of resistance. RESULTS We identified 901 point prevalence surveys from LMICs reporting AMR rates in animals for common indicator pathogens: Escherichia coli, Campylobacter spp., nontyphoidal Salmonella spp., and Staphylococcus aureus. From 2000 to 2018, the proportion of antimicrobial compounds with resistance higher than 50% (P50) increased from 0.15 to 0.41 in chickens and from 0.13 to 0.34 in pigs and plateaued between 0.12 and 0.23 in cattle. Global maps of AMR (available at resistancebank.org) show hotspots of resistance in northeastern India, northeastern China, northern Pakistan, Iran, eastern Turkey, the south coast of Brazil, Egypt, the Red River delta in Vietnam, and the areas surrounding Mexico City and Johannesburg. Areas where resistance is just starting to emerge are Kenya, Morocco, Uruguay, southern Brazil, central India, and southern China. Uncertainty in our predictions was greatest in the Andes, the Amazon region, West and Central Africa, the Tibetan plateau, Myanmar, and Indonesia. Dense geographical coverage of point prevalence surveys did not systematically correlate with the presence of hotspots of AMR, such as in Ethiopia, Thailand, Chhattisgarh (India), and Rio Grande do Sul (Brazil). The highest resistance rates were observed with the most commonly used classes of antimicrobials in animal production: tetracyclines, sulfonamides, and penicillins. CONCLUSION The portfolio of antimicrobials used to raise animals for food is rapidly getting depleted, with important consequences for animal health, farmers’ livelihoods, and potentially for human health. Regions affected by the highest levels of AMR should take immediate actions to preserve the efficacy of antimicrobials that are essential in human medicine by restricting their use in animal production. In some middle-income countries, particularly in South America, surveillance must be scaled up to match that of low-income African countries that are currently outperforming them despite more limited resources. Policy-makers coordinating the international response to AMR may consider sparing African countries from the most aggressive measures to restrict access to veterinary drugs, which may undermine livestock-based economic development and rightfully be perceived as unfair. However, in regions where resistance is starting to emerge, there is a window of opportunity to limit the rise of resistance by encouraging a transition to sustainable animal farming practices. High-income countries, where antimicrobials have been used on farms since the 1950s, should support this transition—for example, through a global fund to subsidize improvement in farm-level biosafety and biosecurity.

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Global trends in antimicrobial resistance in animals in low- and middle-income countries

http://www.experts.com/content/articles/Ewen-Todd-Food%20Worker%20paper%205.pdf

Outbreaks where food workers have been implicated in the spread of foodborne disease. Part 5. Sources of contamination and pathogen excretion from infected persons.

Recent trends in the determination of biogenic amines in fermented beverages – A review

Current food safety issues are deleteriously reshaping the life style of the population in the developing world. Socioeconomic status of the population in poorer economies is one of the major determinants to delineate the availability of safe food to the vulnerable population. Assessment of the prevalence of foodborne illness in developing world is the most neglected area to control disease. Botulism, Shigellosis, Campylobacteriosis, Escherichia coli infection, Staphylococcus aureus infection, Salmonellosis, Listeriosis and Cholerae are extensively prevalent and pose a major threat to human health in underdeveloped communities. The existing food safety status of many African, South Asian, Central, and South American developing countries is distressing therefore; it seems much timely to highlight the areas for the improvement to ensure the supply of safe food to the population in these regions. Extensive literature search at PubMed, Science Direct and Medline was carried out during the current year to catch on relevant data from 1976 to date, using selective terms like food safety, South East Asia, Africa, Central and South America, and foodborne illness etc. Efforts were made to restrict the search to low income countries of these regions with reference to specific foodborne pathogens. This report briefly discusses the present food safety situation in these developing countries and associated consequences as prime issues, suggesting foodborne illness to be the most distressing threat for human health and economic growth.

Microbiological food safety: a dilemma of developing societies.

Enterotoxigenic and antibiotic resistance determination of Staphylococcus aureus strains isolated from food handlers in Gaborone, Botswana.

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.

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Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Detection and quantification of biogenic amines in fermented food products sold in Botswana.

Prevalence and antimicrobial susceptibility of Salmonella isolated from a variety of raw meat sausages in Gaborone (Botswana) retail stores.

The microbial quality and predominant bacterial groups of three fermented beverages was investigated. The bacteria associated with sorghum beer, sour milk (madila/amasi) and sour maize beverage (mageu/mahewu) were determined using standard microbiological techniques. The predominant microorganisms were screened for the production of four biogenic amines using decarboxylase broth. Sorghum beer had the highest bacterial counts with sour maize beverage having the least bacterial counts. Hafnia alvei isolated from sour milk was found to be a major histamine and putrescine producer with 21.2 and 17.56 mg/100 ml respectively. On the other hand, the most important cadaverine producers were Pantoea citrea and Hafnia alvei with19.27 and 18.75 mg/100 ml respectively. Enterococcus faecium and Enterococcus faecalis isolated from sour milk were found to be prolific tyramine producers with 35.5 and 20.07 mg/100 ml respectively. The Bacillus species isolated from all fermented food products were found to be weak histamine producers. The study also revealed that production of biogenic amines was not a widely distributed property among the lactic acid bacteria as previously documented for other fermented food products. Based on the results, it was concluded that sour maize beverage was the safest fermented food product in terms of the microbial quality and presence of biogenic amine producing bacteria.

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Maitshwarelo Ignatius Matsheka

Papers

Enterotoxigenic and antibiotic resistance determination of Staphylococcus aureus strains isolated from food handlers in Gaborone, Botswana.

Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Detection and quantification of biogenic amines in fermented food products sold in Botswana.

Prevalence and antimicrobial susceptibility of Salmonella isolated from a variety of raw meat sausages in Gaborone (Botswana) retail stores.

Biogenic amine producing bacteria associated with three different commercially fermented beverages in Botswana