Periodic Reporting for period 1 - ARBUATEM (Antibiotic resistant bacteria and genes, associated with urban agriculture in Low and Middle Income Countries: Ecological and medical perspectives)
Reporting period: 2015-10-01 to 2017-09-30
• The first objective was to conduct representative sampling of wastewaters and
soils with samples that represented all the investigated areas.
• The second objective was to assess physical-chemical characteristics of collected
samples, and pollution by selected antibiotics. This was to evaluate the influence of abiotic factors and antibiotic pressure on the dynamics of antibiotic-resistant bacteria and antibiotic-resistance genes.
• The third objective was to identify the underlying commonalities / similarities in
antibiotic resistant bacteria community structures in wastewaters and soils. This information was to further allow understanding of the influence of wastewater irrigation on the potential establishment of bacterial phyla, which are known to include strains that can act as facultative or opportunistic human pathogen.
• The fourth objective was to identify antibiotic resistant genes and evaluate their
abundance in wastewaters and soils. That was to allow a description of antibiotic resistant genes of medical interest, their taxonomic position, and development under continuous pollution.
• The fifth objective was to identify plasmid amplicons of clinical relevance. This was to give a broader insight into mobile genetic elements involved in the dissemination of transmissible antibiotic resistance genes.
1.2.1 Work package 1: Sampling, physical-chemical analysis, and antibiotics residues assessment.
We conducted two representative samplings (October 2015, and June-July 2016) in the investigated areas (Cameroon (Yaounde and Ngaoundere); Burkina Faso (Ouagadougou)). The physical and chemical analysis of the collected samples were done at the University of Trier (Germany), during the secondment of Bougnom under the supervision of Prof Sören Thiele-Bruhn. The outputs have been delivered.
1.2.2 Work package 2: Direct sequencing, flow cytometry and construction of metagenomic libraries.
We successfully extracted DNA from wastewater and soil samples. Extracted DNA was used to conduct sequenced based metagenomics. Shotgun metagenomic sequencing was conducted at ARK-Genomics (University of Edinburgh) and the outputs were delivered. Bougnom used the corresponding bioinformatic pipeline necessary to analyse the data. Flow cytometry was substituted with direct isolation and antibiotic susceptibility testing, using culture based bacterial isolation methods. This was because the samples were affected by the long freezing period.
1.2.3 Work package 3: Identification of ARGs and their genomic contexts, and 1.2.4 Work package 4: Biostatistics and Data Management.
We successfully identified ARGs and their genomic contexts from the wastewaters using the appropriate bioinformatic pipeline. We are currently analysing the data from soil DNA sequencing. A detailed Data Management Plan was published on our portal (Section 6
The fellow has acquired new professional skills in the form of research techniques, scientific oral and written communications, supervision and project management to become an independent researcher.