The role of wastewater in surveillance and emergence of antibiotic resistant bacteria

Abstract

As antibiotic resistance spreads among bacterial pathogens, it reduces treatment options and increases treatment failures of infectious diseases. Strategies employed to reduce this spread or adapt to its consequences need to be based on reliable surveillance data which is lacking in many countries, often due to limited resources. Wastewater contains pooled excreted bacteria, including common pathogens such as Escherichia coli, from the population connected to the sewers. Hence, analysis of wastewater has the potential to be used as a resource-efficient surveillance system for antibiotic resistance. In the sewers, human-associated bacteria are also mixed with environmental bacteria and exposed to many substances known to induce horizontal gene transfer (HGT), a major driver for the acquisition of antibiotic resistance in bacteria. The studies presented in this thesis aimed to develop and assess several ways in which the analysis of wastewater samples could be used to provide clinically relevant antibiotic resistance data and evaluate the effects of wastewater on HGT. The resistance rates of E. coli from wastewaters were determined. Additionally, the abundance of different carbapenemase-producing Enterobacterales (CPE) and antibiotic resistance genes (ARGs) were quantified in wastewater. Resistance rates in wastewater E. coli were strongly correlated with resistance rates in clinical isolates and the detection of CPE in wastewater was coherent with the detection of similar CPE in the contributing population. The concentrations of some carbapenemase genes (namely blaOXA-48, blaNDM and blaKPC) were in accordance with the occurrence of CPE carrying those genes in wastewater. Further, a rise of blaOXA-48 in wastewater preceded detection of corresponding CPE in patients, indicating that monitoring of ARGs in wastewater could serve as an early warning system. Hence, it is noteworthy that many ARGs of emerging concern (cfr, optrA, mcr-1, mcr-3, mcr-4, mcr-5, sul4 and gar), which have almost never been detected in Swedish clinical samples, were detected regularly in wastewater. A HGT assay, where a recipient strain was mixed with a complex donor bacterial community, was used to measure the rate of acquisition of ARGs in the presence of wastewater. Municipal wastewater had no detectable effect on HGT but exposure to hospital wastewater could promote antibiotic resistance. Overall, this thesis provides evidence supporting the use of antibiotic resistance data from wastewater analyses as a valuable complement to traditional clinical surveillance. Additionally, the thesis highlights a possible role of hospital wastewater in the emergence of antibiotic resistant bacteria.