Emergence and Co-selection of Antibiotic Resistance in the Environment

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandlingForskning

Antibiotic-resistant pathogens have become a major public health concern, complicating treatment of infectious diseases. The environment has been recognized as a potential risk factor for the emergence and transmission of antibiotic resistance to human pathogens, and this risk may be intensified by anthropogenic activities, such as dispersal of antibiotic resistance from sewage sludge to farmland or pollution of the environment with antibiotics or other selective agents. Heavy metals may for instance co-select for antibiotic resistance e.g. due to genetic linkages between resistances and may, in some cases, provide more efficient selective agents than antibiotics due to their non-degradable nature. However, many knowledge gaps still exist regarding the environmental dimension of antibiotic resistance. This PhD thesis aimed at investigating the emergence and (co)-selection of antibiotic resistance in different environmental settings with special emphasis on the impact of sewage sludge amendment on the soil bacterial resistome, aquaculture systems as a source for antibiotic resistance and heavy metals as co-selecting agents in soil environments. In manuscript I, we took advantage of an agricultural field trial in Sweden to investigate the longterm (36 years) impact of sewage sludge (SS) application on the soil bacterial resistome (i.e., resistance genes in the soil bacterial community). The study was conducted by investigating selective pressures in the soil combined with detailed investigations on the soil bacterial resistome using both metagenomics and resistance typing of soil bacterial isolates. Furthermore, in manuscript II, we used the same soil to construct soil microcosms spiked with different levels of Cu (0-1000 μg g-1) and Zn (0-5000 μg g-1) to investigate if long-term farmland application of SS increased the ability of these metals to co-select antibiotic resistance genes (ARGs) quantified using a high-throughput qPCR (HTqPCR) chip. Collectively, the results from the two studies indicated a negligible risk for a build-up of antibiotic resistance in SS fertilized soil, and SS did not stimulate the potential for metal-induced co-selection of antibiotic resistance. SS may thus be safely used as an organic fertilizer thereby providing future opportunities for closing the urban-rural nutrient cycle, at least for countries like Denmark and Sweden, where SS used for farmland application is of high quality. In manuscript III, we explored the impact of increasing Cu concentrations on co-selection of antibiotic resistance in Chinese agricultural paddy soil. The Cu-induced selection pressure was determined by measuring bioavailable Cu using a whole-cell bacterial Cu bioreporter and by measuring pollution-induced community tolerance (PICT) using the [3H]leucine incorporation technique and by determining the fraction of Cu resistant soil bacterial isolates. The effect of the increasing Cu concentration on co-selection of antibiotic resistance was explored by phenotypical resistance screening 333 bacterial isolates to Cu and six classes of antibiotics. Additionally, we explored the abundance of ARGs and mobile genetic elements (MGEs) as well as the bacterial community composition in the soils using HT-qPCR chip analysis and 16S rRNA gene amplicon sequencing. Both bioavailable Cu concentrations and bacterial community tolerance to Cu increased with increasing soil Cu concentrations. The observed PICT response corresponded to a significant shift in the bacterial community composition, accompanied by a significant shift in the ARGs prevalence pattern. Elevated soil Cu levels resulted in a significantly increased fraction of Cu and antibiotic-resistant bacterial isolates, and a significant co-occurrence between resistances was observed in the isolates demonstrating co-selection of antibiotic-resistant bacteria. Moreover, the number of detected MGEs in the soil was increased by the elevated Cu levels, indicating a potential for mobilization of ARGs. Our findings suggest that Cu pollution of paddy soil may constitute a significant concern for public health, as paddy soil forms the base for irrigated rice production thereby causing possible transmission of antibiotic resistance to humans. In manuscript IV, we investigated the prevalence and diversity of ARGs and MGEs in Pangasius and Tilapia commercial aquaculture ponds from four regions of Bangladesh using HT- qPCR chip analysis. Our results revealed a high prevalence of ARGs and MGEs in the aquaculture ponds, with a total of 160 ARGs and 10 MGEs detected across all samples (n=33). Multidrug resistance genes were the most frequently encountered ARGs, followed by ARGs to β-lactams, aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLSB). The detected ARGs exhibited a significant (R2=0.34, p<0.001) biogeographical prevalence pattern (i.e., separation based on geographic origin), potentially mediated by feed type as different feed types were used in different regions. Furthermore, we compared the commercial ponds to strictly managed aquaculture systems maintained by Bangladesh Agricultural University (BAU) without use of antibiotics. Ponds managed by BAU had a lower abundance and diversity of ARGs than the commercial ponds, suggesting that proper management like regular water exchange and use of probiotics instead of antibiotics may mitigate antibiotic resistance in aquaculture systems. Aquaculture constitutes a high-risk environment for dissemination of antibiotic resistance, as it is directly linked to humans via the food chain. Mitigation of antibiotic resistance development and dissemination in aquaculture should, therefore, be of top priority and may be achieved by better aquaculture management practices, as demonstrated in this study. Collectively, this thesis provides novel insights into the risks for environmental selection and dissemination of antibiotic resistance in various anthropogenic impacted environments.
OriginalsprogEngelsk
ForlagDepartment of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen
Antal sider243
StatusUdgivet - 2021

ID: 273704237