Presence of carbapenem-resistant bacteria in soils affected by illegal waste dumps

Abstract

The carbapenem-resistant bacteria (CRB) are currently at the top of the WHO priority list of bacteria that pose the greatest threat to human health. Considering that soil is one of the important environments for the emergence of antibiotic-resistant bacteria, we isolated and quantified cultivable CRB in soils across Croatia, including ones affected by illegal dumps. We cultivated CRB at two temperatures, distinguishing between the intrinsically resistant CRB (37°C, mostly Stenotrophomonas spp.) and the ones that are presumably human-associated and clinically relevant (42°C, Acinetobacter sp., Enterobacteriaceae, Burkholderia spp.). Our study demonstrated that distinguishing between the two offers a better insight into the diversity of CRB in the environment. The ones cultivated at 37°C were found in almost all soil samples, while the presumably clinically relevant ones were absent from uncontaminated pasture and grassland, indicating that human-associated CRB are unlikely to be found in soils spared from anthropogenic influence.

Urban and agricultural soils in Southern California are a reservoir of carbapenem‐resistant bacteria

“…In the future, as we expand our studies to additional soil samples and locations, it will be interesting to analyze our samples at both 37°C and 42°C to compare the abundance and diversity of CRB obtained at both temperatures. However, of the 40 CRB isolates identified and characterized in the present study, only 11 of them (from 3 different soil samples) were S. maltophilia (Tables 2 and 3), and we were able to isolate, among other CRB, carbapenem‐resistant (CR) Cupriavidus, and Pseudomonas strains, as reported by Hrenovic et al (2019) at 42°C. These findings suggest that, although S. maltophilia may be an important contributor to the abundance and wide distribution of CRB found in the soils we analyzed, other CRB were also an important factor.…”

“…Moreover, although different soil locations were tested in both studies, our findings, as well as those from Djenadi et al (2018), suggest that at 37°C, using MacConkey medium instead of CHROMagar might contribute to isolating more diverse CRB, even without using 42°C to suppress the growth of S. maltophilia . Also, CR Pseudomonas were the most abundant (15 out of 40 CRB identified in our study) CRB we found, compared to only one CR Pseudomona s isolate identified by Hrenovic et al (2019) at 42°C. Although further studies analyzing the same soil samples with both growth media and temperatures are necessary, this finding suggests that isolation of CRB at 42°C may not only suppress the growth of S. maltophilia , but also of closely related Pseudomonas .…”

“…As is further discussed below, S. maltophilia are widespread in soil and other environments, and are intrinsically resistant to carbapenems (Brooke, 2012; Harmon et al, 2019; Tacão et al, 2015; Youenou et al, 2015). They also found that isolating CRB at 42°C, which suppresses the growth of S. maltophilia , increased the diversity of CRB recovered from their samples, including CRB of potential anthropogenic origin (Hrenovic et al, 2019). In the future, as we expand our studies to additional soil samples and locations, it will be interesting to analyze our samples at both 37°C and 42°C to compare the abundance and diversity of CRB obtained at both temperatures.…”

“…Even though there is no established relationship between the broad use of β‐lactams or extended‐spectrum β‐lactams and resistance to carbapenems, the use of these and other drugs is predicted to cause selection favoring carbapenem resistance in the environment (Meletis, 2016; Mollenkopf et al, 2017). Recent findings of CRB in environmental samples from Europe, Africa, Asia, and North America (Adelowo, Vollmers, Mäusezahl, Kaster, & Müller, 2018; Ash, Mauck, & Morgan, 2002; Aubron, Poirel, Ash, & Nordmann, 2005; Di, Jang, Unno, & Hur, 2017; Girlich, Poirel, & Nordmann, 2010; Harmon et al, 2019; Henriques et al, 2012; Hrenovic et al, 2019; Isozumi et al, 2012; Mills & Lee, 2019; Poirel et al, 2012; Potron, Poirel, Bussy, & Nordmann, 2011; Sivalingam, Pote, & Prabakar, 2019; Tacão, Correia, & Henriques, 2015; Zou et al, 2020; Zurfluh, Hachler, Nuesch‐Inderbinen, & Stephan, 2013) seem to support this hypothesis. However, further studies are needed to fully understand the role of the environment as a reservoir of CRB and carbapenem resistance genes.…”

“…However, recent studies in soil and related environmental samples from Africa and Europe suggest that soil may be an underappreciated reservoir of CRB. For example, CRB including CP‐CRB have been isolated from agricultural and nonagricultural soil samples from Algeria, Spain, England, Germany, Denmark, and Norway (Gudeta et al, 2016) and Croatia (Hrenovic et al, 2019), as well as from swine and poultry farms from Germany (Borowiak et al, 2017; Fischer et al, 2013), and natural soil samples from Algeria (Djenadi, Zhang, Murray, & Gaze, 2018), among other locations.…”