Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields

Abstract

Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach and 6/60 (10%) of soil samples using culture-based techniques. Whole genome sequencing (WGS) analysis identified the spinach isolates as belonging to the hypervirulent clade 5, sequence type (ST) 11, ribotypes (RT) 078 and 126 and carried the genes encoding toxins A, B and CDT. The soil isolates belonged to clade 1 with different toxigenic ST/RT (ST19/RT614, ST12/RT003, ST46/RT087, ST16/RT050, ST49/RT014/0) strains and one non-toxigenic ST79/RT511 strain. Antimicrobial resistance to erythromycin (one spinach isolate), rifampicin (two soil isolates), clindamycin (one soil isolate), both moxifloxacin and rifampicin (one soil isolate), and multi-drug resistance to erythromycin, vancomycin and rifampicin (two soil isolates) were observed using the E test, although a broader range of resistance genes were detected using WGS. Although the sample size was limited, our results demonstrate the presence of C. difficile in horticulture and provide further evidence that there are multiple sources and dissemination routes for these bacteria.

Clostridioides difficile, a New “Superbug”

“…An important finding in this report is that the authors observed a similar distribution of ribotypes between clinical, hospital and environmental isolates (RT014/020, 002, 078/126 as most common) with the exception that ribotype 027, which was significantly more common in the clinical isolates compared with the environmental isolates [105]. A recent study detected ST11 (RT078 and RT126) strains in spinach [106]. A very large study covering a wide part of the world (North America (Mexico), Central America (Peru, Guatemala), South America (Brazil), Europe (France, Germany, Italy), and Asia (Taiwan, India)) showed high C. difficile contamination rates (~24%), which were similar for healthcare buildings and non-healthcare buildings.…”

Clostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective

“…Furthermore, RT001 and RT014 were one of the most frequently detected in isolates from poultry meat in Germany [19]. RT014 was also detected in soil samples being located next to a dairy farm [45]. RT014 and RT020 were the predominant RT among soil isolates obtained from home gardens in Western Australia [46] and poultry feces [20].…”

Usefulness of Capillary Gel Electrophoresis-Based PCR for Detection of Clostridioides difficile Strains with Hypervirulent Ribotypes

“…Capillary electrophoresis offers an improved separation of amplified nucleic acid fragments, leading to enhanced sensitivity of the assay compared to traditional agarose electrophoresis [52,55,56]. Therefore, it may lead to relatively fast recognition of CDI hospital outbreaks worldwide [57][58][59] and facilitate antimicrobial resistant strains' elimination [60][61][62][63], including those derived from children [64], the environment, plants and animals [65][66][67][68][69][70][71]. As it has been previously proven, an ineffective decontamination with non-optimal time of exposure or a concentration of sporicidal disinfectants may result in an extensive C. difficile strain transmission [60].…”