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AbstractBackgroundThe crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.MethodsThis was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistant E. coli isolated from stool samples from both humans and cattle in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/42 from human and 8/42 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes.ResultsThe genomes of the human E. coli generally clustered together and away from those of cattle origin. The E. coli isolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from the E. coli population from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump.A high variation of virulence genes was registered among the E. coli genomes from humans than those of cattle origin.ConclusionThe E. coli of human and cattle origin are largely independent with different ancestral origins. Limited sharing of strains and resistance genes presents a challenge to the hypothesis that AMR in humans is as a result of antibiotic misuse on the farm.

ABSTRACTBackgroundAntibiotic use as growth promoters for livestock is presumed to be a major contributor to the acquisition of antimicrobial resistance (AMR) genes in humans, yet data evaluating AMR patterns in the setting of animal exposure are limited to observational studies that do not capture data from prior to livestock introduction.MethodsWe performed a feasibility study by recruiting a subset of women in a delayed-start randomized controlled trial of small-scale chicken farming in order to examine the prevalence of clinically-relevant AMR genes. Stool samples were obtained at baseline and one year from five intervention women who received chickens at the start of the study, six control women who did not receive chickens until the end of the study, and from chickens provided to the control group at the end of the study. Stool was screened for 87 clinically significant AMR genes using a commercially available qPCR array (Qiagen).ResultsChickens harbored 23 AMR genes from classes also found in humans as well as vancomycin and additional β-lactamase resistance genes. After one year of exposure to chickens, six new AMR genes were detected in controls and seven new AMR genes were detected in the intervention group. Women who had direct contact with the chickens sampled in the study had greater similarities in AMR resistance gene patterns to chickens than those who did not have direct contact with chickens sampled (p = 0.006). There was a trend towards increased similarity in AMR gene patterns with chickens at one year (p = 0.12).ConclusionsChickens and humans in this study harbored AMR genes from many antimicrobial classes at both baseline and follow up timepoints. Studies designed to evaluate human AMR genes in the setting of animal exposure should account for high baseline AMR rates, and consider collecting concomitant animal samples, human samples, and environmental samples over time to determine the directionality and source of AMR genes.Trial registration: ClinicalTrials.gov Identifier: NCT02619227

AbstractQuality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.Key MessageA 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.

ABSTRACTThe growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 400 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among all chicken Salmonella including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified replicons through WGS (ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p= 0.0017). We conclude that MDR Salmonella highlights the risks posed to the animals, environment, and humans for infection. Implementing a robust integrated surveillance system in Uganda will help monitor MDR to help control infectious threats.

AbstractThe nutritional and economic potentials of livestock systems are compromised by the emergence and spread of antimicrobial resistance. A major driver of resistance is the misuse and abuse of antimicrobial drugs. The likelihood of misuse may be elevated in low- and middle-income countries where limited professional veterinary services and laissez faire access to drugs are assumed to promote non-prudent practices (e.g., self-administration of drugs). The extent of these practices, as well as the knowledge and attitudes motivating them, are largely unknown within most agricultural communities in low- and middle-income countries. The main objective of this study was to document dimensions of knowledge, attitudes and practices related to antimicrobial use and antimicrobial resistance in livestock systems and identify the livelihood factors associated with these dimensions. A mixed-methods ethnographic approach was used to survey households keeping layers in Ghana (N=110) and Kenya (N=76), pastoralists keeping cattle, sheep, and goats in Tanzania (N=195), and broiler farmers in Zambia (N=198), and Zimbabwe (N=298). Across countries, we find that it is individuals who live or work at the farm who draw upon their knowledge and experiences to make decisions regarding antimicrobial use and related practices. Input from animal health professionals is rare and antimicrobials are sourced at local, privately owned agrovet drug shops. We also find that knowledge, attitudes, and particularly practices significantly varied across countries, with poultry farmers holding more knowledge, desirable attitudes, and prudent practices compared to pastoralists households. Multivariate models showed that variation is related to several factors, including education, disease dynamics on the farm, and sources of animal health information. Study results emphasize that interventions to limit antimicrobial resistance must be founded upon a bottom-up understanding of antimicrobial use at the farm-level given limited input from animal health professionals and under-resourced regulatory capacities within most low- and middle-income countries. Establishing this bottom-up understanding across cultures and production systems will inform the development and implementation of the behavioral change interventions to combat AMR globally.

AbstractIn the high Andes, environmental and socio-economic drivers are transforming land use and presumably affecting thein situconservation of potato (Solanumspp.). To monitor the use and conservation of intraspecific diversity, systematic and comparative studies across land-use systems are needed. We investigated the spatial-temporal dynamics of potato in two contrasting landscapes of Peru’s central Andes: a highland plateau (Huancavelica) vs. an eastern slope (Pasco). We examined household-level areal allocations, altitudinal distribution, sectoral fallowing practices, and the conservation status for three main cultivar groups: (i) bred varieties, (ii) floury landraces, and (iii) bitter landraces. Mixed methods were used to survey 323 households and the 1,101 potato fields they managed in 2012–2013. We compared the contemporary altitudinal distribution of landraces with 1975–1985 altimeter genebank data from the International Potato Center. We show that intensification occurs in each landscape through adaptations of traditional management practices while maintaining high intraspecific diversity. Access to land and production end use (sale vs. consumption) significantly affected smallholder management and differentiated the landscapes. Total areas in Huancavelica and Pasco were allocated to 82.9% vs. 74.2% floury landraces, 9.2% vs. 25.7% bred varieties, and 7.9% vs. 0.1% bitter landraces. In market-oriented Pasco, fields in sectoral fallows between 3,901 m and 4,116 m above sea level consistently contained the highest levels of landrace diversity. The bulk of diversity in subsistence-oriented Huancavelica occurred between 3,909 m and 4,324 m outside sectoral fallows. Most of the unique landraces documented were scarce across households: 45.4% and 61.7% respectively in Huancavelica and Pasco. Bred varieties showed the widest (1,100 m) and bitter landraces the narrowest (400 m) altitudinal distributions. Potato cultivation has moved upward by an average of 306 m since 1975. Landrace diversity is versatile but unevenly distributed across landscapes. This requires adaptive ways to incentivizein situconservation.

AbstractIntroductionAdherence to antiretroviral therapy (ART) is critical in order to achieve viral suppression, one of three UNAIDS targets set for achievement before 2020. One of the main barriers to adherence is the long distance between patient residences and healthcare facilities. We designed an intervention, Mobile Antiretroviral Therapy and HIV care (MAP-HC) in rural southwestern Uganda aimed to reduce travel distance and hypothesized that MAP-HC would improve ART adherence and rates of viral load suppression.MethodsThe study was conducted at two sites, Kitagata and Itojo Hospitals, and these are public health facilities located in rural southwestern Uganda. Patients who lived >5km from the hospital were provided the option to participate. For each hospital, we identified 4 health centres in the catchment area to serve as site for the mobile pharmacy. Each site was visited once a month to provide ART refills, adherence counseling and treatment of other illnesses. We measured patient waiting time, adherence and viral load suppression before and after the intervention.ResultsWe conducted baseline assessment among 292 patients at the two hospitals. The mean waiting time at Kitagata Hospital changed from 4.48 hours before the intervention but increased to 4.76 hours after the intervention (p=0.13). The proportion of patients who missed an ART dose in the last 30 days dropped from 20% at baseline to 8.5% at 12 months after the intervention (p=0.009). The proportion of patients with detectable viral load from 19.9% to 7.4% after the intervention (p=0.001).ConclusionsOur study has showed that a mobile pharmacy intervention in rural Uganda is feasible and resulted in improvement in adherence and viral load suppression. Although it did not reduce patient waiting time at the clinic, we recommend a scale-up of this intervention in rural areas where patients face challenges of transportation to the clinic.