Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

Abstract

Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3–6 antibiotic resistance genes (ARG) conferring resistance to 2–4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.

Hitherto-Unnoticed Self-Transmissible Plasmids Widely Distributed among Different Environments in Japan

“…S7). Currently, there are a few plasmids in the PromA group carrying accessory genes: in PromAα, pSB102 with mercury resistance genes ( 31 ); in PromAβ-1, pALTS28 with multidrug resistance genes ( 32 ) and pS28-3 with a florfenicol resistance gene ( 33 ); and in PromAγ, four plasmids, pPBL-H3_BS2-2, pPBL-H3_BS4-2, pBPS33-2, and pEN1 with linuron degradative genes ( 34 ). The genetic structures of PromA plasmids with accessory genes were reported to be unstable ( 34 ), which could be one of the reasons why the obtained PromA plasmids did not possess any accessory genes.…”

Antibiotic resistomes and microbial communities in biosolid fertilizers collected from two Canadian wastewater treatment plants in a 10-years interval-potential risks to food chains?

“…Particularly, ermB has the highest target copy numbers (the lowest average Ct value), a typical characteristic gene detected in urban sewages in North America and Europe (Hendriksen et al, 2019). Numerous studies on the characterization of ARG or ARB in wastewater have been conducted over the past decades using various methods to facilitate the detection of ARGs in biosolids or sludge (Viau and Peccia, 2009a;Novo et al, 2013;Agga et al, 2015;Yergeau et al, 2016;Li et al, 2020;Law et al, 2021;Zielinski et al, 2021;Jankowski et al, 2022). In contrast to these studies, we investigated the changes of the antibiotic resistomes at two different facilities over the 1A and Supplementary Table S1), indicating that Gram-positive bacteria containing these ARGs were probably present in both WWTPs at the early sampling date but not 10 years later or the wastewater treatment efficiencies improved over time and subsequently eliminated the bacteria.…”

“…Humans can acquire antibiotic-resistant bacteria (ARB) from various sources, including infections, food, and water intake (Singer et al, 2016;Bennani et al, 2020;Nappier et al, 2020;Larsson and Flach, 2021). During the last decades, a new concern has arisen regarding the critical role of the food chain played in the transmission of ARB to humans (Greig et al, 2015;Bennani et al, 2020;Panel, et al, 2021), since food can be easily contaminated by ARGs and/or ARB derived from different environmental sources including agriculture (Law et al, 2021;Zielinski et al, 2021). Biosolids, nutrient-rich organic fertilizer, and soil conditioner, obtained from the solid effluents after municipal wastewater treatment, have been considered as an alternative source of nutrients to chemical fertilizer and have been widely and directly applied to land, including forestry and farmland, in almost every province in Canada and throughout the United States (Lu et al, 2012;Egan, 2013;Mason-Renton and Luginaah, 2016;Whitehouse et al, 2022).…”

“…Moreover, many bacteria within the sewage matrix could carry ARGs, and some of these ARGs get concentrated during treatment processes resulting in a higher concentration of ARGs in biosolids (Munir et al, 2011). Consequently, biosolids have also been considered a reservoir of ARGs and many pathogenic bacteria (Viau and Peccia, 2009a;Agga et al, 2015;Yergeau et al, 2016;Al-Gheethi et al, 2018;Law et al, 2021;Jankowski et al, 2022). And it is possible that ARGs, ARB and pathogenic bacteria could enter food chains through biosolid application to crop lands (EFSA BIOHAZ Panel et al, 2021).…”

Antibiotic resistance in Escherichia coli from Animals, Food and Humans

“…The phenomenon is called horizontal gene transfer which takes place asexually via plasmids, transposons, and gene cassettes and the process of conjugation, transformation and transduction. Receiving hereditary material from other bacteria is not based on selection according to the species, and for that reason, a new genetic strain of the bacterium can be obtained (Poirel et al 2018;Law et al 2021).…”