Environmental antimicrobial resistance is associated with faecal pollution in Central Thailand’s coastal aquaculture region

Contaminants of Emerging Concern in the Lower Volta River, Ghana, West Africa: The Agriculture, Aquaculture, and Urban Development Nexus

“…Nevertheless, and perhaps not surprisingly given the size of the Volta River, the diffuse inputs, and the fact that it was the dry season with limited runoff, when normalized by total 16S gene copy numbers, overall ARG concentrations were relatively low (Figure 2B), with other researchers often observing much higher normalized ARG concentrations in rivers in Thailand, Bolivia, India, China, and Finland impacted by wastewater (see Agramont et al, 2020; Devarajan et al, 2016; Thongsamer et al, 2021) or aquaculture facilities (see Gao et al, 2018; Muziasari et al, 2014; Xiong et al, 2015). Given the number of small and large villages/towns along the Volta River, it is possible that fecal contamination is a source of ARGs, which is thought to be a primary driver of ARG contamination in freshwater globally (Agramont et al, 2020; Almakki et al, 2019; Devarajan et al, 2016; Ho et al, 2021; Thongsamer et al, 2021; Vikesland et al, 2019). Because it was the dry season, however, it is also possible that overland fecal contamination was limited.…”

“…Nevertheless, insufficient and failing infrastructure, including sanitation infrastructure, remains a major obstacle to achieving this goal, a problem shared by many other low‐ and medium‐income countries (Asem‐Hiablie et al, 2013; Egbi et al, 2020; Gwenzi & Chaukura, 2018). Rural communities in Ghana rely on a patchwork of latrines, household septic systems, and underperforming sewage‐treatment facilities for the treatment of human waste (Egbi et al, 2020), all serving as potential sources of antibiotic‐resistant microorganisms and antibiotic‐resistance genes (ARGs; Agramont et al, 2020; Ho et al, 2021; Thongsamer et al, 2021; Vikesland et al, 2019). Hormones (Aneck‐Hahn et al, 2009) and pharmaceuticals (see review by Fekadu et al, 2019) also end up in surface water.…”

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

“…Zooplanktonic biomass can be harvested with meshes having 200 µm openings [36], while the biomass of algae [74] and cyanobacteria [48] can be isolated by medium to large volume centrifugation (0.05 to 1 L). Most studies targeting bacteria and archaea filtered between 0.1 and 4 L of water through membranes with 0.22 µm pore size to capture the biomass [27,37,47,50,54,59,63,66,[68][69][70][71]73]. Filtration can take hours to complete [27], and sometimes water prefiltration through membranes with a pore size between 0.4 and 11 µm was used to remove suspended solids [37,76].…”

“…Amplification of specific genes or genome regions of interest, targeted with appropriate primers, additionally assures that the full capacity of the MinION is devoted to sequencing these genes or regions. Several studies used full-length 16S rRNA gene amplicon sequencing to characterize communities of bacteria and archaea [27,29,38,48,50,54,56,63,65,66,68,71], mostly with ONT's 16S barcoding kit. Long-range PCR amplicons spanning 3 kb of the rDNA cassette were used for the detection of algal bloom organisms [74].…”

“…Several 16S rRNA gene amplicon studies used ONT's FASTQ 16S workflow to classify bacteria in drinking water [54], groundwater [50], river water [27,63,65,66,68,71], wastewater [38,66,71], aquaculture ponds [68], and sea lice [29]. Van der Loos et al [59] used EPI2ME and Kraken2 with three different reference databases (SILVA [98], Greengenes [99] and NCBI) and recommended assigning taxonomy of nanopore-derived long-reads with Kraken2 and the SILVA database in seaweed-microbiome studies to avoid misidentifications of cyanobacteria due to chloroplast contamination.…”