Clostridium difficile in soil conditioners, mulches and garden mixes with evidence of a clonal relationship with historical food and clinical isolates

Abstract

With rates of community-associated Clostridium difficile infection (CA-CDI) increasing worldwide, potential reservoirs/sources of C. difficile in the community are being sought. Since C. difficile is found in animal manure and human biosolids, which are composted for agricultural purposes, composted products could be a source. In this study, the presence of C. difficile in composted products, and their genetic relatedness to other previously isolated strains from humans, root vegetables and the environment in Western Australia, was investigated. Overall, C. difficile was found in 22.5% (16/71) of composted products [29.7% (11/37) of soil conditioners, 16.7% (2/12) of mulches and 13.6% (3/22) of garden mixes]. Fifteen C. difficile PCR ribotypes (RTs) were identified, the most common toxigenic strains being RTs 020 and 056. Clostridium difficile RT 056 is commonly associated with CDI in humans and has also been isolated from cattle, root vegetables and the environment (veterinary clinics and lawn) in Australia. High-resolution coregenome analysis of 29 C. difficile RT 056 strains revealed clonal relationships between isolates derived from humans, vegetables, composted products and the environment. These findings provide support for an intricate transmission network between human, food and the environment, further highlighting the importance of a 'One Health' approach for managing CDI.

Genetically related Clostridium difficile from water sources and human CDI cases revealed by whole‐genome sequencing

“…In Australia, C. difficile has been isolated from a diverse range of non‐human sources/reservoirs in the community including calves (prevalence = 56%) (Knight et al ., 2013), lambs (7%) (Knight and Riley, 2013), piglets (67%) (Knight et al ., 2015b), public lawn (59%) (Moono et al ., 2017), soil conditioners (30%), mulches (17%), garden mixes (14%) (Lim et al ., 2020), hospital gardens (60%) (Perumalsamy et al ., 2019), home gardens (67%) (Shivaperumal et al ., 2020), and potatoes (56%), beetroots (22%), onions (6%) and carrots (5%) (Lim et al ., 2018). However, the prevalence and molecular epidemiology of C. difficile in Australian waters have not been investigated.…”

Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile

“…In addition, CDI occurs independent from healthcare at increasing incidence (Ofori et al, 2018), but reservoirs and pathways of transmission outside of the hospital environment are incompletely understood (Warriner et al, 2017;Rodriguez Diaz et al, 2018). Toxigenic C. difficile seems widespread in various environments, since it was recovered from domestic wastewater (Moradigaravand et al, 2018;Numberger et al, 2019) and river sediments (Zidaric et al, 2010), from compost (Janezic et al, 2020;Lim et al, 2020a), soil (Janezic et al, 2016) and root vegetables (Lim et al, 2018;Tkalec et al, 2019). It was also found to colonize various mammals and birds, including wildlife, pets and livestock (Weese, 2020).…”

“…Toxigenic C . difficile seems widespread in various environments, since it was recovered from domestic wastewater (Moradigaravand et al ., 2018; Numberger et al ., 2019) and river sediments (Zidaric et al ., 2010), from compost (Janezic et al ., 2020; Lim et al ., 2020a), soil (Janezic et al ., 2016) and root vegetables (Lim et al ., 2018; Tkalec et al ., 2019). It was also found to colonize various mammals and birds, including wildlife, pets and livestock (Weese, 2020).…”

Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogenClostridioides difficile

“…Toxigenic C. difficile seems widespread in various environments, since it was recovered from domestic wastewater (Moradigaravand et al ., 2018; Numberger et al ., 2019) and river sediments (Zidaric et al ., 2010), from retail compost (Lim et al ., 2020), soil (Janezic et al ., 2016) and root vegetables (Lim et al ., 2018; Tkalec et al ., 2019). It was also found to colonize various mammals and birds, including wildlife, pets, and livestock (Weese, 2020).…”

“…In addition, CDI occurs independent from healthcare at increasing incidence (Ofori et al, 2018), but reservoirs and pathways of transmission outside of the hospital environment are incompletely understood (Warriner et al, 2017;Rodriguez Diaz et al, 2018). Toxigenic C. difficile seems widespread in various environments, since it was recovered from domestic wastewater (Moradigaravand et al, 2018;Numberger et al, 2019) and river sediments (Zidaric et al, 2010), from retail compost (Lim et al, 2020), soil (Janezic et al, 2016) and root vegetables (Lim et al, 2018;Tkalec et al, 2019). It was also found to colonize various mammals and birds, including wildlife, pets, and livestock (Weese, 2020).…”