Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

In the HTML version of this Letter, the affiliations for authors Andrew S. Azman, Dhirendra Kumar and Thandavarayan Ramamurthy were inverted (the PDF and print versions of the Letter were correct); the affiliations have been corrected online.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

BACKGROUND: Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. METHODS: We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. RESULTS: We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. CONCLUSIONS: Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.

A Critical Review of Aflatoxin Contamination of Peanuts in Malawi and Zambia: The Past, Present, and Future.

Peanut (Arachis hypogaea L.) is an important crop in Malawi and Zambia. The crop is valued for soil improvement in cereal-based cropping systems, for improving the livelihoods of farming households who consume it and also sell it for cash, and for earning foreign exchange when exported. Research and development efforts have resulted in an increase in both peanut production area and productivity. However, a key challenge that still needs to be solved in these countries is how to produce peanuts with acceptable levels of aflatoxin contamination. Data continues to show that aflatoxin continues to be a problem in both formal and informal trade. As a result, unlike 30 years ago, most of the peanut trade has now shifted to domestic and regional markets that do not restrict the sale of aflatoxin-contaminated peanuts. Impacts of aflatoxin contamination on health and also on the full cost burden of control are not well documented. Technologies are available for mitigating against aflatoxin contamination. The advantages, disadvantages, and gaps associated with these technologies are discussed. Considerable money and effort continues to be invested in Malawi and Zambia into mitigating aflatoxin contamination, but evidence of long-term success is limited. Based on past and current initiatives, the prospects of eliminating aflatoxin in the near future at the household level and in trade are not promising.

Tropical surface water quality studies: Implications for the aquatic fate of N-methyl carbamate pesticides.

Water quality assessment was conducted on the Ruiru River, a tributary of an important tropical river system in Kenya, to determine baseline river conditions for studies on the aquatic fate of N-methyl carbamate (NMC) pesticides. Measurements were taken at the end of the long rainy season in early June 2013. Concentrations of copper (0.21-1.51 ppm), nitrates (2.28-4.89 ppm) and phosphates (0.01-0.50 ppm) were detected at higher values than in uncontaminated waters, and attributed to surface runoff from agricultural activity in the surrounding area. Concentrations of dissolved oxygen (8-10 ppm), ammonia (0.02-0.22 ppm) and phenols (0.19-0.83 ppm) were found to lie within normal ranges. The Ruiru River was found to be slightly basic (pH 7.08-7.70) with a temperature of 17.8-21.2°C. The half-life values for hydrolysis of three NMC pesticides (carbofuran, carbaryl and propoxur) used in the area were measured under laboratory conditions, revealing that rates of decay were influenced by the electronic nature of the NMCs. The hydrolysis half-lives at pH 9 and 18°C decreased in the order carbofuran (57.8 h) > propoxur (38.5 h) > carbaryl (19.3 h). In general, a decrease in the electron density of the NMC aromatic ring increases the acidity of the N-bound proton removed in the rate-limiting step of the hydrolysis mechanism. Our results are consistent with this prediction, and the most electron-poor NMC (carbaryl) hydrolyzed fastest, while the most electron-rich NMC (carbofuran) hydrolyzed slowest. Results from this study should provide baseline data for future studies on NMC pesticide chemical fate in the Ruiru River and similar tropical water systems.

Understanding variability in crop response to fertilizer and amendments in sub-Saharan Africa.

Improved understanding of soil fertility factors limiting crop productivity is important to develop appropriate soil and nutrient management recommendations in sub-Saharan Africa. Diagnostic trials were implemented in Kenya, Malawi, Mali, Nigeria and Tanzania, as part of the African Soils Information Service (AfSIS) project, to identify soil fertility constraints to crop production across various cropping systems and soil fertility conditions. In each country, one to three sites of 10 km × 10 km were included with each site having 12-31 field trials. The treatments tested included a control, an NPK treatment, three treatments in which the N, P and K nutrients were omitted one at a time from the NPK treatment, and three treatments in which secondary and micronutrients (Ca, Mg, S, Zn and B) simply referred here as multi-nutrients, manure and lime were added to the NPK. The field trials were conducted for 1-2 seasons; the test crop was maize except in Mali where sorghum was used. Nitrogen was limiting in all sites and generally the most limiting nutrient except in Sidindi (Kenya) and Kontela (Mali) where P was the most limiting. The general pattern in Kiberashi (Tanzania) shows none of the nutrients were limiting. K is mainly limiting in only one site (Mbinga) although incidences of K limitation were seen in almost all sites. Addition of multi-nutrients and manure further improved the yields of NPK in most sites. Cluster analyses revealed that maize crop in 11% of fields were highly responsive to nitrogen application, 25% (i.e., 21% poor and 4% fertile) 'non-responsive' to any nutrient or soil amendment, 28% being 'low responsive' and 36% of 'intermediate response'. This study indicates that constraints to crop production vary considerably even within a site, and that addressing limitations in secondary and micronutrients, and increasing soil carbon can improve response to fertilizers. For sustainable crop production intensification in smallholder farming systems in SSA, there is need to develop management strategies to improve efficiency of fertilizer use and of other inputs, recognizing the site-specific nutrient response patterns at various spatial scales.

Ceftriaxone-resistant Salmonella enterica serotype typhimurium sequence type 313 from Kenyan patients is associated with the blaCTX-M-15 gene on a novel IncHI2 plasmid.

Multidrug-resistant bacteria pose a major challenge to the clinical management of infections in resource-poor settings. Although nontyphoidal Salmonella (NTS) bacteria cause predominantly enteric self-limiting illness in developed countries, NTS is responsible for a huge burden of life-threatening bloodstream infections in sub-Saharan Africa. Here, we characterized nine S. Typhimurium isolates from an outbreak involving patients who initially failed to respond to ceftriaxone treatment at a referral hospital in Kenya. These Salmonella enterica serotype Typhimurium isolates were resistant to ampicillin, chloramphenicol, cefuroxime, ceftriaxone, aztreonam, cefepime, sulfamethoxazole-trimethoprim, and cefpodoxime. Resistance to ß-lactams, including to ceftriaxone, was associated with carriage of a combination of blaCTX-M-15, blaOXA-1, and blaTEM-1 genes. The genes encoding resistance to heavy-metal ions were borne on the novel IncHI2 plasmid pKST313, which also carried a pair of class 1 integrons. All nine isolates formed a single clade within S. Typhimurium ST313, the major clone of an ongoing invasive NTS epidemic in the region. This emerging ceftriaxone-resistant clone may pose a major challenge in the management of invasive NTS in sub-Saharan Africa.

Enhancing sustainable agri-food systems using multi-nutrient fertilizers in Kenyan smallholder farming systems.

Persistent food insecurity in the global south has triggered calls for sustainable development worldwide. Moreover, more than a quarter of the world's population suffers from micronutrient deficiencies or hidden hunger. The population bulge, declining soil fertility and inadequate/inappropriate use of farm inputs in Sub-Saharan Africa place it in a precarious position. Multi-nutrient fertilizer blends have been mooted as a key innovation in closing yield gaps and boosting food and nutrition security. This study assessed the extent of multi-nutrient fertilizer blends utilization and yield response across agroecological zones and their on-farm profitability under Kenyan smallholder farmer conditions. We collected data through a detailed household survey conducted in eight counties in Kenya representative of high, medium, and low productivity zones using a sample of 1094 smallholder farmers. Multi-nutrient fertilizers increased maize yields significantly (P < 0.05), eliciting a 400% yield increase compared to the control and 108% greater maize yield than conventional fertilizers in the high potential zone. Conversely, at 3.7 t/ha conventional fertilizers elicited a significant (P < 0.05) yield response in Irish potatoes in the high potential areas. Multi-nutrient fertilizers increased on-farm profitability of crops, specifically for potato production systems where a benefit: cost ratio (BCR) of more than 2 was observed. Farmers may break even when they use multi-nutrient fertilizers on maize particularly in the low potential areas. Therefore, there is considerable potential for multi-nutrient fertilizers to increase crop productivity while being economically viable across agroecological zones and cropping systems. However, the uptake of multi-nutrient fertilizers among farmers is quite low across the country, except for small pockets where limited interventions have been carried out. This calls for sustained efforts to scale multi-nutrient fertilizers with a focus on clear messaging that stresses the need to apply appropriate rates of various nutrients including the secondary nutrients and micro-nutrients.

Campylobacter positivity and public health risks in live bird markets in Busia, Kenya: A value chain analysis.

Live bird markets (LBMs) provide integral hubs for 95% of poultry produced for food. Surveillance systems in LBMs serving smallholder farmers in sub-saharan Africa are often non-functional, and data about public health risks and emerging pathogens are lacking. Studies in Kenya have reported 29-44% Campylobacter prevalence in poultry. We analysed such LBMs in Kenya for likely transmission of Campylobacter from poultry to humans. We conducted a cross-sectional survey among 186 live poultry traders (LPTs) in 14 LBMs in a region with widespread backyard poultry systems. A pretested structured questionnaire was administered to all LPTs having regular contacts with poultry to gather market data and risk information on campylobacteriosis. Campylobacter was detected in individual cloacal cultures and identified through PCR. The median score obtained from the outcome of risk assessment dichotomized respondents into high and low risk categories. We performed logistic regression at 95% confidence interval (CI) to compare market characteristics and Campylobacter positivity to risk categories to identify LBM-associated public health risks. Markets had a median of 13 traders, and mean age of 46.3 ± 13.7 years. Majority 162/186 (87.1%) were males. Market behavioural processes by LPTs varied: Only 58.6% LPTs held bird species separate; onsite slaughter (38.7%); encountered sick-bird (93%) and dead-bird (83%) amidst limited health inspection (31.2%). Campylobacter positivity in live birds was 43/112 (38.4%, 95% CI: 29.4-48.1). Risk information on campylobacteriosis was low 41/114 (36%, 95% CI: 27.2-45.5). Sanitary risks were related to accumulation of litter (adjusted prevalence odds ratio [aPOR]: 19.67, 95% CI: 3.01-128.52). Accessing hand-wash facilities (aPOR: .32, 95% CI: .13-.78) and access to information (aPOR: .24, 95% CI: .09-.61) were protective. Sanitary risks were related to poor hygiene. LBMs could be central surveillance sites for Campylobacter. Public health authorities/actors should consider appropriate targeting to improve sanitary measures and Campylobacter control strategies.

Aflatoxin in cereals and groundnut from small holder farming households in Malawi.

Aflatoxin contamination in commonly consumed cereals and nuts may place children at higher risk of stunting and adults at risk of developing liver cancer. This study investigated knowledge on aflatoxins and the level of aflatoxin B1 contamination in commonly consumed cereals and nuts in Malawi. It also included an examination of the proportion of cereals and nuts contaminated above regulatory maximum limits. Aflatoxin contamination in samples was assessed using an enzyme-linked immunosorbent assay (ELISA) method. Less than half of all households knew that consumption of aflatoxin contaminated grain is associated with stunting and lowered immunity. Sorghum samples were the most contaminated and millet the least contaminated. Aflatoxin contamination was highest in southern Malawi and least in northern Malawi. Observed results indicate that this population is at risk of poor health due to lack of knowledge and aflatoxin exposure. Strategies to address contamination should therefore include a comprehensive education campaign to increase knowledge and promote accessible strategies.

Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.

Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.

Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.

High-throughput selection, enumeration, electrokinetic manipulation, and molecular profiling of low-abundance circulating tumor cells using a microfluidic system.

A circulating tumor cell (CTC) selection microfluidic device was integrated to an electrokinetic enrichment device for preconcentrating CTCs directly from whole blood to allow for the detection of mutations contained within the genomic DNA of the CTCs. Molecular profiling of CTCs can provide important clinical information that cannot be garnered simply by enumerating the selected CTCs. We evaluated our approach using SW620 and HT29 cells (colorectal cancer cell lines) seeded into whole blood as a model system. Because SW620 and HT29 cells overexpress the integral membrane protein EpCAM, they could be immunospecifically selected using a microfluidic device containing anti-EpCAM antibodies immobilized to the walls of a selection bed. The microfluidic device was operated at an optimized flow rate of 2 mm s(-1), which allowed for the ability to process 1 mL of whole blood in <40 min. The selected CTCs were then enzymatically released from the antibody selection surface and hydrodynamically transported through a pair of Pt electrodes for conductivity-based enumeration. The efficiency of CTC selection was found to be 96% ± 4%. Following enumeration, the CTCs were hydrodynamically transported at a flow rate of 1 µL min(-1) to an on-chip electromanipulation unit, where they were electrophoretically withdrawn from the bulk hydrodynamic flow and directed into a receiving reservoir. Using an electric field of 100 V cm(-1), the negatively charged CTCs were enriched into an anodic receiving reservoir to a final volume of 2 µL, providing an enrichment factor of 500. The collected CTCs could then be searched for point mutations using a PCR/LDR/capillary electrophoresis assay. The DNA extracted from the CTCs was subjected to a primary polymerase chain reaction (PCR) with the amplicons used for a ligase detection reaction (LDR) to probe for KRAS oncogenic point mutations. Point mutations in codon 12 of the KRAS gene were successfully detected in the SW620 CTCs for samples containing <10 CTCs in 1 mL of whole blood. However, the HT29 cells did not contain these mutations, consistent with their known genotype.

Integrated continuous flow polymerase chain reaction and micro-capillary electrophoresis system with bioaffinity preconcentration.

An integrated and modular DNA analysis system is reported that consists of two modules: (i) A continuous flow polymerase chain reaction (CFPCR) module fabricated in a high T(g) (150°C) polycarbonate substrate in which selected gene fragments were amplified using biotin and fluorescently labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones as opposed to heating and cooling large thermal masses typically performed in batch-type thermal reactors. (ii) µCE (micro-capillary electrophoresis) module fabricated in poly(methylmethacrylate) (PMMA), which utilized a bioaffinity selection and purification bed (2.9 µL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to electrophoretic sorting. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed, where they were extracted onto the surface of micropillars. The affinity bed was also fabricated in PMMA and was populated with an array of microposts (50 µm width; 100 µm height) yielding a total surface area of ∼117 mm(2). This solid-phase extraction (SPE) process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (K(d) = 10(-15) M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single-stranded DNA released for injection into a 7-cm-long µCE channel for size-based separations and fluorescence detection. The utility of the system was demonstrated using Alu DNA typing for gender and ethnicity determinations as a model. Compared with the traditional cross-T injection procedure typically used for µCE, the affinity pre-concentration and injection procedure generated signal enhancements of 17- to 40-fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation.

Integrated microfluidic systems for DNA analysis.

The potential utility of genome-related research in terms of evolving basic discoveries in biology has generated widespread use of DNA diagnostics and DNA forensics and driven the accelerated development of fully integrated microfluidic systems for genome processing. To produce a microsystem with favorable performance characteristics for genetic-based analyses, several key operational elements must be strategically chosen, including device substrate material, temperature control, fluidic control, and reaction product readout. As a matter of definition, a microdevice is a chip that performs a single processing step, for example microchip electrophoresis. Several microdevices can be integrated to a single wafer, or combined on a control board as separate devices to form a microsystem. A microsystem is defined as a chip composed of at least two microdevices. Among the many documented analytical microdevices, those focused on the ability to perform the polymerase chain reaction (PCR) have been reported extensively due to the importance of this processing step in most genetic-based assays. Other microdevices that have been detailed in the literature include those for solid-phase extractions, microchip electrophoresis, and devices composed of DNA microarrays used for interrogating DNA primary structure. Great progress has also been made in the areas of chip fabrication, bonding and sealing to enclose fluidic networks, evaluation of different chip substrate materials, surface chemistries, and the architecture of reaction conduits for basic processing steps such as mixing. Other important elements that have been developed to realize functional systems include miniaturized readout formats comprising optical or electrochemical transduction and interconnect technologies. These discoveries have led to the development of fully autonomous and functional integrated systems for genome processing that can supply "sample in/answer out" capabilities. In this chapter, we focus on microfluidic systems that are composed of two or more microdevices directed toward DNA analyses. Our discussions will primarily be focused on the integration of various processing steps with microcapillary electrophoresis (µCE) or microarrays. The advantages afforded by fully integrated microfluidic systems to enable challenging applications, such as single-copy DNA sequencing, single-cell gene expression analysis, pathogen detection, and forensic DNA analysis in formats that provide high throughput and point-of-analysis capabilities will be discussed as well.

Hospital-based evidence on cost-effectiveness of brucellosis diagnostic tests and treatment in Kenyan hospitals.

Hospitals in Kenya continue to use the Febrile Antigen Brucella Agglutination Test (FBAT) to diagnose brucellosis, despite reports showing its inadequacy. This study generated hospital-based evidence on the performance and cost-effectiveness of the FBAT, compared to the Rose Bengal Test (RBT).Twelve hospitals in western Kenya stored patient serum samples that were tested for brucellosis using the FBAT, and these were later re-tested using the RBT. Data on the running time and cost of the FBAT, and the treatment prescribed for brucellosis, were collected. The cost-effectiveness of the two tests, defined as the cost in US Dollars ($) per Disability Adjusted Life Year (DALY) averted, was determined, and a basic sensitivity analysis was run to identify the most influential parameters. Over a 6-month period, 180 patient serum samples that were tested with FBAT at the hospitals were later re-tested with RBT at the field laboratory. Of these 24 (13.3%) and 3 (1.7%) tested positive with FBAT and RBT, respectively. The agreement between the FBAT and RBT was slight (Kappa = 0.12). Treatment prescribed following FBAT positivity varied between hospitals, and only one hospital prescribed a standardized therapy regimen. The mean $/DALY averted when using the FBAT and RBT were $2,065 (95% CI $481-$6,736) and $304 (95% CI $126-$604), respectively. Brucellosis prevalence was the most influential parameter in the cost-effectiveness of both tests. Extrapolation to the national level suggested that an estimated $338,891 (95% CI $47,000-$1,149,000) per year is currently spent unnecessarily treating those falsely testing positive by FBAT. These findings highlight the potential for misdiagnosis using the FBAT. Furthermore, the RBT is cost-effective, and could be considered as the mainstay screening test for human brucellosis in this setting. Lastly, the treatment regimens must be harmonized to ensure the appropriate use of antibiotics for treatment.

Microchip electrophoresis of Alu elements for gender determination and inference of human ethnic origin.

We performed a series of multi-locus PCRs followed by the rapid and efficient microchip electrophoretic sorting of Alu products with LIF detection. Five polymorphic human-specific Alu insertions (RC5, A1, PV92, TPA and ACE) were used for inference of human ethnicity and two monomorphic Alu insertions for sex typing, one fixed on the X chromosome (AluSTXa) and the other on the Y chromosome (AluSTYa). These markers were used to generate unique DNA profiles for five different DNA samples. The PCR-based assays used primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. A1, RC5, PV92, TPA and ACE were used for ethnicity determinations and have two alleles, each indicating the presence (+) or absence (-) of the Alu element on the paired chromosomes, which results in three genotypes (+/+, +/- or -/-). RC5 and A1 did not show ethnic heterogeneity resulting in a homozygous (-/-) genotype, which correctly inferred that DNA samples originating from a Caucasian male and an Asian male were not of African ancestry. The results from the five Alu markers indicated that these Alu loci could assist in identifying the individual's ethnicity using microchip electrophoresis in under 15 min of separation time. Using microchip electrophoresis and mixed genotype ratios, male DNA-to-female DNA of 1:9, corresponding to a ratio of Y-to-X chromosomes of 1:19, was also detected for both AluSTXa and AluSTYa to provide gender identification without requiring separation of female from male cells prior to the assay.

The Genome of Caenorhabditis bovis.

The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans has also become a model for parasitic nematodes despite being only distantly related to most parasitic species. All of the ∼65 Caenorhabditis species currently in culture are free-living, with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species that has been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa, where it is associated with the disease bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism. However, as C. bovis is not in laboratory culture, it remains little studied. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolated C. bovis from the ear of adult female Zebu. We sequenced the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and used the data to generate a chromosome-scale draft genome sequence. We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identified expansions in several gene families that have been implicated in parasitism in other nematode species. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.

Functional Biology and Molecular Mechanisms of Host-Pathogen Interactions for Aflatoxin Contamination in Groundnut (Arachis hypogaea L.) and Maize (Zea mays L.).

Aflatoxins are secondary metabolites produced by soilborne saprophytic fungus Aspergillus flavus and closely related species that infect several agricultural commodities including groundnut and maize. The consumption of contaminated commodities adversely affects the health of humans and livestock. Aflatoxin contamination also causes significant economic and financial losses to producers. Research efforts and significant progress have been made in the past three decades to understand the genetic behavior, molecular mechanisms, as well as the detailed biology of host-pathogen interactions. A range of omics approaches have facilitated better understanding of the resistance mechanisms and identified pathways involved during host-pathogen interactions. Most of such studies were however undertaken in groundnut and maize. Current efforts are geared toward harnessing knowledge on host-pathogen interactions and crop resistant factors that control aflatoxin contamination. This study provides a summary of the recent progress made in enhancing the understanding of the functional biology and molecular mechanisms associated with host-pathogen interactions during aflatoxin contamination in groundnut and maize.

Comparison of Crop Rotation for Verticillium Wilt Management and Effect on Pythium Species in Conventional and Organic Strawberry Production.

The effects of broccoli and lettuce rotations on population densities of Verticillium dahliae and Pythium spp. in soil and on strawberry (Fragaria × ananassa) growth, yield, and Verticillium wilt were evaluated in conventional and organic production systems in California for 2 years. Under both management systems, strawberry was planted after two successive crops of broccoli or lettuce. The control treatment in the conventional field was strawberry planted in soils fumigated with methyl bromide + chloropicrin. Preplant densities of V. dahliae and Pythium sp. did not differ in these fields. At the end of the second broccoli crop, V. dahliae densities in conventional plots had declined by 44% in both years. In contrast, after the second broccoli crop, densities in organic fields decreased 47% in 2000 and 25% in 2001. In general, there were no differences in V. dahliae inoculum densities in organic and conventional plots following lettuce rotations. After the second vegetable production cycle, population densities of V. dahliae in broccoli rotated organic (24 CFU/g of soil in 2000 and 27 CFU/g of soil in 2001) or conventional (23 CFU/g of soil in 2000 and 19 CFU/g of soil in 2001) fields were significantly lower than those in lettuce rotated organic (40 CFU/g of soil in 2000 and 42 CFU/g of soil in 2001) or conventional (39 CFU/g of soil in 2000 and 35 CFU/g of soil in 2001) fields. However, crop rotation treatments had no consistent effect on the inoculum densities of Pythium spp. Canopy diameters of strawberry plants grown in rotation with broccoli were not different from those in fumigated control plots, whereas those from lettuce plots were 10% smaller. Strawberry plant nutrient analysis showed that fertilizer inputs into organic or conventional production were not responsible for the observed differences in plant size. Increases in strawberry yields were not consistent between years. Verticillium wilt incidence on strawberry was 12 to 24% lower in fields rotated with broccoli compared with fields rotated with lettuce. Wilt severity on strawberry was 22 to 36% lower in fields rotated with broccoli compared with those rotated with lettuce. The strategy of using broccoli rotation coupled with postharvest incorporation of broccoli residue continues to show promise as a tool in the management of Verticillium wilt in both conventional and organic strawberry production systems.