Prevalence, Antimicrobial Resistance and Toxin-Encoding Genes of Clostridioides difficile from Environmental Sources Contaminated by Feces

Molecular Epidemiology of Clostridioides difficile Infections in Patients Hospitalized in 2017-2019 at the Central Teaching Hospital of Medical University of Lodz, Central Poland

Background/Objectives:Clostridioides difficile infection (CDI) represents a significant public health challenge globally, driven by its increasing prevalence, hypervirulent strains like ribotype 027 (RT027), and growing antibiotic resistance. This study aimed to evaluate the prevalence of RT027 and analyze molecular markers of vancomycin and metronidazole resistance in stool samples from CDI patients hospitalized in Poland between 2017 and 2019. Methods: A total of 200 stool samples from confirmed CDI cases were analyzed for the presence of RT027, vanA (vancomycin resistance), and nim (metronidazole resistance) genes. DNA was extracted, and a polymerase chain reaction (PCR) was conducted using specific primers. Statistical associations between RT027 and resistance genes were evaluated using chi-square tests and logistic regression. Results: RT027 was detected in 14% of samples. The vanA gene, indicative of vancomycin resistance, was found in 52.5% of samples, while the nim gene, associated with metronidazole resistance, was present in 1.5% of cases. Co-occurrence of RT027 with vanA was not statistically significant. The study revealed no significant association between RT027 and vanA. Also, no significant association was observed between RT027 and nim due to the latter's low prevalence. Conclusions: This study highlights a concerning prevalence of vanA among CDI cases, indicating widespread vancomycin resistance and challenging current treatment guidelines. While RT027 prevalence was moderate, no significant associations with vancomycin or metronidazole resistance were observed. These findings emphasize the need for molecular surveillance and improved antimicrobial stewardship to manage CDI effectively.

Efficacy of UV-C 254 nm Light and a Sporicidal Surface Disinfectant in Inactivating Spores from Clostridioides difficile Ribotypes In Vitro

Clostridioides difficile is widely recognised as one of the most common causes of healthcare-associated C. difficile infections due to the ability of spores to survive for prolonged periods in the hospital environment. This study aimed to evaluate the efficacy of UV-C 254 nm light in the inactivation of the spores of different C. difficile ribotypes on brain heart infusion (BHI) agar plates or in phosphate-buffered saline (PBS) with varying spore densities. Furthermore, the effectiveness of a sporicidal surface disinfectant against C. difficile spores was determined on different surfaces. Spore suspensions of different C. difficile strains in the range of 105-107 colony-forming units (CFUs) mL-1 were inoculated on BHI agar plates or in PBS and exposed to UV-C light for up to 30 min. Additionally, a spore suspension of 103-105 CFUs was spread over a 1 cm2 test area on different surfaces, and sporicidal surface wipes were used according to the manufacturer's instructions. The findings demonstrated that spores of C. difficile ribotypes exhibited a complete reduction in log10 CFU on BHI agar plates and PBS following 20 min of exposure to a UV-C dose of 2208 mJ cm-2. The surface wipes with sporicidal properties demonstrated efficacy in reducing the number of C. difficile spores on the Formica, stainless steel, and plastic surfaces by 2.03-3.53 log10. The present study demonstrates that moist surfaces or liquids can enhance the efficacy of UV-C treatment in reducing C. difficile spores. This approach may be applicable to the surfaces of healthcare facilities and to water disinfection systems.

Antibiotic Resistance in the Elderly: Mechanisms, Risk Factors, and Solutions

Antibiotic resistance presents a critical challenge in healthcare, particularly among the elderly, where multidrug-resistant organisms (MDROs) contribute to increased morbidity, mortality, and healthcare costs. This review focuses on the mechanisms underlying resistance in key bacterial pathogens and highlights how aging-related factors like immunosenescence, frailty, and multimorbidity increase the burden of infections from MDROs in this population. Novel strategies to mitigate resistance include the development of next-generation antibiotics like teixobactin and cefiderocol, innovative therapies such as bacteriophage therapy and antivirulence treatments, and the implementation of antimicrobial stewardship programs to optimize antibiotic use. Furthermore, advanced molecular diagnostic techniques, including nucleic acid amplification tests and next-generation sequencing, allow for faster and more precise identification of resistant pathogens. Vaccine development, particularly through innovative approaches like multi-epitope vaccines and nanoparticle-based platforms, holds promise in preventing MDRO infections among the elderly. The role of machine learning (ML) in predicting resistance patterns and aiding in vaccine and antibiotic development is also explored, offering promising solutions for personalized treatment and prevention strategies in the elderly. By integrating cutting-edge diagnostics, therapeutic innovations, and ML-based approaches, this review underscores the importance of multidisciplinary efforts to address the global challenge of antibiotic resistance in aging populations.

Non-human Clostridioides difficile Reservoirs and Sources: Animals, Food, Environment

Clostridioides difficile is ubiquitous and is found in humans, animals and in variety of environments. The substantial overlap of ribotypes between all three main reservoirs suggests the extensive transmissions. Here we give the overview of European studies investigating farm, companion and wild animals, food and environments including water, soil, sediment, wastewater treatment plants, biogas plants, air, and households. Studies in Europe are more numerous especially in last couple of years, but are still fragmented in terms of countries, animal species, or type of environment covered. Soil seem to be the habitat of divergent unusual lineages of C. difficile. But the most important aspect of animals and environment is their role in C. difficile transmissions and their potential as a source for human infection is discussed.

Prophage Carriage and Genetic Diversity within Environmental Isolates of Clostridioides difficile

Clostridioides difficile is an important human pathogen causing antibiotic-associated diarrhoea worldwide. Besides using antibiotics for treatment, the interest in bacteriophages as an alternative therapeutic option has increased. Prophage abundance and genetic diversity are well-documented in clinical strains, but the carriage of prophages in environmental strains of C. difficile has not yet been explored. Thus, the prevalence and genetic diversity of integrated prophages in the genomes of 166 environmental C. difficile isolates were identified. In addition, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems were determined in the genomes of prophage regions. Predicted prophages and CRISPR-Cas systems were identified by using the PHASTER web server and CRISPRCasFinder, respectively. Phylogenetic relationships among predicated prophages were also constructed based on phage-related genes, terminase large (TerL) subunits and LysM. Among 372 intact prophages, the predominant prophages were phiCDHM1, phiCDHM19, phiMMP01, phiCD506, phiCD27, phiCD211, phiMMP03, and phiC2, followed by phiMMP02, phiCDKM9, phiCD6356, phiCDKM15, and phiCD505. Two newly discovered siphoviruses, phiSM101- and phivB_CpeS-CP51-like Clostridium phages, were identified in two C. difficile genomes. Most prophages were found in sequence types (STs) ST11, ST3, ST8, ST109, and ST2, followed by ST6, ST17, ST4, ST5, ST44, and ST58. An obvious correlation was found between prophage types and STs/ribotypes. Most predicated prophages carry CRISPR arrays. Some prophages carry several gene products, such as accessory gene regulator (Agr), putative spore protease, and abortive infection (Abi) systems. This study shows that prophage carriage, along with genetic diversity and their CRISPR arrays, may play a role in the biology, lifestyle, and fitness of their host strains.

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

Clostridioides difficile is the most important pathogen causing antimicrobial-associated diarrhea and has recently been recognized as a cause of community-associated C. difficile infection (CA-CDI). This study aimed to characterize virulence factors, antimicrobial resistance (AMR), ribotype (RT) distribution and genetic relationship of C. difficile isolates from diverse fecally contaminated environmental sources. C. difficile isolates were recovered from different environmental samples in Northern Germany. Antimicrobial susceptibility testing was determined by E-test or disk diffusion method. Toxin genes (tcdA and tcdB), genes coding for binary toxins (cdtAB) and ribotyping were determined by PCR. Furthermore, 166 isolates were subjected to whole genome sequencing (WGS) for core genome multi-locus sequence typing (cgMLST) and extraction of AMR and virulence-encoding genes. Eighty-nine percent (148/166) of isolates were toxigenic, and 51% (76/148) were positive for cdtAB. Eighteen isolates (11%) were non-toxigenic. Thirty distinct RTs were identified. The most common RTs were RT127, RT126, RT001, RT078, and RT014. MLST identified 32 different sequence types (ST). The dominant STs were ST11, followed by ST2, ST3, and ST109. All isolates were susceptible to vancomycin and metronidazole and displayed a variable rate of resistance to moxifloxacin (14%), clarithromycin (26%) and rifampicin (2%). AMR genes, such as gyrA/B, blaCDD-1/2, aph(3')-llla-sat-4-ant(6)-la cassette, ermB, tet(M), tet(40), and tetA/B(P), conferring resistance toward fluoroquinolone, beta-lactam, aminoglycoside, macrolide and tetracycline antimicrobials, were found in 166, 137, 29, 32, 21, 72, 17, and 9 isolates, respectively. Eleven "hypervirulent" RT078 strains were detected, and several isolates belonged to RTs (i.e., RT127, RT126, RT023, RT017, RT001, RT014, RT020, and RT106) associated with CA-CDI, indicating possible transmission between humans and environmental sources pointing out to a zoonotic potential.