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

Abstract

Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 104 cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

Freshwater and Marine Environments in California Are a Reservoir of Carbapenem-Resistant Bacteria

“…Regarding the Gram-positive CRB isolated in this study, seven out of eight were Enterococcus sp., and one isolate was preliminarily identified as Paenibacillus lautus (Figures 7 and 8). Interestingly, no Gram-positives were identified in our previous water study [43], although we found Enterococcus species in our survey for CRB in soil [44], which usually has a larger bacterial load. Our findings in this study suggest that the broader type of ecosystems sampled here, and especially the addition of an enrichment step (seven out of the eight Gram-positive CRB were obtained from the sub-samples subject to enrichment), contributed to the better isolation of Gram-positive CRB.…”

“…To identify carbapenemase-producing CRB isolates, we utilized the CarbaNP assay as previously described [43,44] to detect carbapenem hydrolysis. Briefly, we performed the CarbaNP assay [56][57][58] following the CLSI guidelines [48] and using 6 mg/mL of meropenem.…”

“…More recently, a study from our group examined the distribution and characteristics of CRB in ponds and lakes in the Los Angeles, CA area [43]. This study, together with a second study from our group investigating CRB in Southern California soils [44], has revealed that CRB and carbapenemase genes are more widespread than previously thought. However, further studies are still needed to better understand the spread, diversity, and characteristics of CRB in the environment in the US.…”

Short-Term Effects of Experimental Fire on Physicochemical and Microbial Properties of a Mediterranean Cambisol

“…The CRB are the main focus of bio-medical scientists due to the emergence of these bacteria as human pathogens. However, new research focuses are arising concerning their distribution within soil and water environments [46][47][48], as well as in waste-treatment plants [49]. Reports of CRB in soil are relatively scarce [47], but to our knowledge, no studies exist that focused on their survival rate in the soil following wildfires.…”