Diversity and Evolution in the Genome of Clostridium difficile

Modelling diverse sources of Clostridium difficile in the community: importance of animals, infants and asymptomatic carriers

Clostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults and transmission from animal reservoirs. We assessed the role of these transmission routes in maintaining disease and evaluated the recommended classification system for hospital- and community-acquired CDIs. The reproduction number in the hospital was <1 (range: 0.16–0.46) for all scenarios. Outside the hospital, the reproduction number was >1 for nearly all scenarios without transmission from animal reservoirs (range: 1.0–1.34). However, the reproduction number for the human population was <1 if a minority (>3.5–26.0%) of human exposures originated from animal reservoirs. Symptomatic adults accounted for <10% transmission in the community. Under conservative assumptions, infants accounted for 17% of community transmission. An estimated 33–40% of community-acquired cases were reported but 28–39% of these reported cases were misclassified as hospital-acquired by recommended definitions. Transmission could be plausibly sustained by asymptomatically colonised adults and infants in the community or exposure to animal reservoirs, but not hospital transmission alone. Under-reporting of community-onset cases and systematic misclassification underplays the role of community transmission.

Different molecular characteristics and antimicrobial resistance profiles of Clostridium difficile in the Asia-Pacific region

Molecular epidemiology of Clostridium difficile infection (CDI) has been extensively studied in North America and Europe; however, limited data on CDI are available in the Asia-Pacific region. A multicentre retrospective study was conducted in this region. C. difficile isolates were subjected to multilocus sequence typing (ST) and antimicrobial susceptibility testing. Totally, 394 isolates were collected from Hangzhou, Hong Kong, China; Busan, South Korea; Fukuoka, Japan; Singapore; Perth, Sydney, Australia; New York, the United States. C. difficile isolates included 337 toxin A-positive/B-positive/binary toxin-negative (A⁺B⁺CDT^-), 48 A^-B⁺CDT^-, and nine A⁺B⁺CDT⁺. Distribution of dominant STs varied geographically with ST17 in Fukuoka (18.6%), Busan (56.0%), ST2 in Sydney (20.4%), Perth (25.8%). The antimicrobial resistance patterns were significantly different among the eight sites (χ² = 325.64, p < 0.001). Five major clonal complexes correlated with unique antimicrobial resistances. Healthcare-associated (HA) CDI was mainly from older patients with more frequent antimicrobial use and higher A^-B⁺ positive rates. Higher resistance to gatifloxacin, tetracycline, and erythromycin were observed in HA-CDI patients (χ² = 4.76-7.89, p = 0.005-0.029). In conclusion, multiple C. difficile genotypes with varied antimicrobial resistance patterns have been circulating in the Asia-Pacific region. A^-B⁺ isolates from older patients with prior antimicrobial use were correlated with HA-CDI.

High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years

Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.

Molecular Epidemiology and Risk Factors of Clostridium difficile ST81 Infection in a Teaching Hospital in Eastern China

BACKGROUND

The prevalence of Clostridium difficile causes an increased morbidity and mortality of inpatients, especially in Europe and North America, while data on C. difficile infection (CDI) are limited in China.

METHODS

From September 2014 to August 2019, 562 C. difficile isolates were collected from patients and screened for toxin genes. Multilocus sequence typing (MLST) and antimicrobial susceptibility tests by E-test and agar dilution method were performed. A case group composed of patients infected with sequence type (ST) 81 C. difficile was compared to the non-ST81 infection group and non CDI diarrhea patients for risk factor and outcome analyses.

RESULTS

The incidence of inpatients with CDI was 7.06 cases per 10,000 patient-days. Of the 562 C. difficile isolates, ST81(22.78%) was the predominant clone over this period, followed by ST54 (11.21%), ST3 (9.61%), and ST2 (8.72%). Toxin genotype tcdA+tcdB+cdt- accounted for 50.18% of all strains, while 29.54% were tcdA-tcdB+cdt- genotypes. Overall, no isolate was resistant to vancomycin, teicoplanin or daptomycin, and resistance rates to meropenem gradually decreased during these years. Although several metronidazole-resistant strains were isolated in this study, the MIC values decreased during this period. Resistance rates to moxifloxacin and clindamycin remained higher than those to the other antibiotics. Among CDI inpatients, longer hospitalization, usage of prednisolone, suffering from chronic kidney disease or connective tissue diseases and admission to emergency ward 2 or emergency ICU were significant risk factors for ST81 clone infection. All-cause mortality of these CDI patients was 4.92%(n=18), while the recurrent cases accounted for 5.74%(n=21). The 60-day mortality of ST81-CDI was significantly higher than non-ST81 infected group, while ST81 also accounted for most of the recurrent CDI cases.

CONCLUSION

This study revealed the molecular epidemiology and risk factors for the dominant C. difficile ST81 genotype infection in eastern China. Continuous and stringent surveillance on the emerging ST81 genotype needs to be initiated.

cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America

Cfr is a radical S-adenosyl-l-methionine (SAM) enzyme that confers cross-resistance to antibiotics targeting the 23S rRNA through hypermethylation of nucleotide A2503. Three cfr-like genes implicated in antibiotic resistance have been described, two of which, cfr(B) and cfr(C), have been sporadically detected in Clostridium difficile However, the methylase activity of Cfr(C) has not been confirmed. We found cfr(B), cfr(C), and a cfr-like gene that shows only 51 to 58% protein sequence identity to Cfr and Cfr-like enzymes in clinical C. difficile isolates recovered across nearly a decade in Mexico, Honduras, Costa Rica, and Chile. This new resistance gene was termed cfr(E). In agreement with the anticipated function of the cfr-like genes detected, all isolates exhibited high MIC values for several ribosome-targeting antibiotics. In addition, in vitro assays confirmed that Cfr(C) and Cfr(E) methylate Escherichia coli and, to a lesser extent, C. difficile 23S rRNA fragments at the expected positions. The analyzed isolates do not have mutations in 23S rRNA genes or genes encoding the ribosomal proteins L3 and L4 and lack poxtA, optrA, and pleuromutilin resistance genes. Moreover, these cfr-like genes were found in Tn6218-like transposons or integrative and conjugative elements (ICE) that could facilitate their transfer. These results indicate selection of potentially mobile cfr-like genes in C. difficile from Latin America and provide the first assessment of the methylation activity of Cfr(C) and Cfr(E), which belong to a cluster of Cfr-like proteins that does not include the functionally characterized enzymes Cfr, Cfr(B), and Cfr(D).

Clostridioides (Clostridium) Difficile in Food-Producing Animals, Horses and Household Pets: A Comprehensive Review

Clostridioides (Clostridium) difficile is ubiquitous in the environment and is also considered as a bacterium of great importance in diarrhea-associated disease for humans and different animal species. Food animals and household pets are frequently found positive for toxigenic C. difficile without exposing clinical signs of infection. Humans and animals share common C. difficile ribotypes (RTs) suggesting potential zoonotic transmission. However, the role of animals for the development of human infection due to C. difficile remains unclear. One major public health issue is the existence of asymptomatic animals that carry and shed the bacterium to the environment, and infect individuals or populations, directly or through the food chain. C. difficile ribotype 078 is frequently isolated from food animals and household pets as well as from their environment. Nevertheless, direct evidence for the transmission of this particular ribotype from animals to humans has never been established. This review will summarize the current available data on epidemiology, clinical presentations, risk factors and laboratory diagnosis of C. difficile infection in food animals and household pets, outline potential prevention and control strategies, and also describe the current evidence towards a zoonotic potential of C. difficile infection.

Antimicrobial resistance in Clostridium difficile ribotype 017

Introduction: Antimicrobial resistance (AMR) played an important role in the initial outbreaks of Clostridium difficile infection (CDI) in the 1970s. C. difficile ribotype (RT) 017 has emerged as the major strain of C. difficile in Asia, where antimicrobial use is poorly regulated. This strain has also caused CDI outbreaks around the world for almost 30 years. Many of these outbreaks were associated with clindamycin and fluoroquinolone resistance. AMR and selective pressure is likely to be responsible for the success of this RT and may drive future outbreaks.Areas covered: This narrative review summarizes the prevalence and mechanisms of AMR in C. difficile RT 017 and transmission of these AMR mechanisms. To address these topics, reports of outbreaks due to C. difficile RT 017, epidemiologic studies with antimicrobial susceptibility results, studies on resistance mechanisms found in C. difficile and related publications available through Pubmed until September 2019 were collated and the findings discussed.Expert opinion: Primary prevention is the key to control CDI. This should be achieved by developing antimicrobial stewardship in medical, veterinary and agricultural practices. AMR is the key factor that drives CDI outbreaks, and methods for the early detection of AMR can facilitate the control of outbreaks.

Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum

Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.

Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing

BACKGROUND

Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates.

RESULTS

Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes.

CONCLUSIONS

We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.

Isolation and characterization of Clostridium difficile from a small survey of wastewater, food and animals in New Zealand

The objective of this study was to undertake a microbiological survey of foods, animal faeces and wastewater samples for Clostridium difficile, and determine the genotypes and antimicrobial susceptibilities of isolates. A total of 211 samples were tested for C. difficile using culture methods. Thirteen toxigenic C. difficile isolates were obtained; ten from wastewater samples, one each from pig and duck faeces and another from a raw meat product. Eight PCR-ribotypes (RTs) were identified, including two novel RTs (878 and 879). Single-nucleotide polymorphism analysis using WGS data for all isolates provided greater discrimination between C. difficile isolates within the same RT and multilocus sequence typing (MLST) profiles. All C. difficile isolates were found to be susceptible to the first-line human antimicrobials used to treat C. difficile infection. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to report the isolation of Clostridium difficile from animals, food and wastewater in New Zealand (NZ) and provides important data with respect to ribotypes and multilocus sequence typing profiles, whole genome sequence and antimicrobial susceptibilities. The results highlight the need for further investigations into the epidemiology of C. difficile in NZ and to elucidate the role of the environmental and food sources as transmission routes of human infection.

The evolving epidemiology of Clostridium difficile infection in Canadian hospitals during a postepidemic period (2009-2015)

BACKGROUND

The clinical and molecular epidemiology of health care-associated Clostridium difficile infection in nonepidemic settings across Canada has evolved since the first report of the virulent North American pulsed-field gel electrophoresis type 1 (NAP1) strain more than 15 years ago. The objective of this national, multicentre study was to describe the evolving epidemiology and molecular characteristics of health care-associated C. difficile infection in Canada during a post-NAP1-epidemic period, particularly patient outcomes associated with the NAP1 strain.

METHODS

Adult inpatients with C. difficile infection were prospectively identified, using a standard definition, between 2009 and 2015 through the Canadian Nosocomial Infection Surveillance Program (CNISP), a network of 64 acute care hospitals. Patient demographic characteristics, severity of infection and outcomes were reviewed. Molecular testing was performed on isolates, and strain types were analyzed against outcomes and epidemiologic trends.

RESULTS

Over a 7-year period, 20 623 adult patients admitted to hospital with health care-associated C. difficile infection were reported to CNISP, and microbiological data were available for 2690 patients. From 2009 to 2015, the national rate of health care-associated C. difficile infection decreased from 5.9 to 4.3 per 10 000 patient-days. NAP1 remained the dominant strain type, but infection with this strain has significantly decreased over time, followed by an increasing trend of infection with NAP4 and NAP11 strains. The NAP1 strain was significantly associated with a higher rate of death attributable to C. difficile infection compared with non-NAP1 strains (odds ratio 1.91, 95% confidence interval [CI] 1.29-2.82). Isolates were universally susceptible to metronidazole; one was nonsusceptible to vancomycin. The proportion of NAP1 strains within individual centres predicted their rates of health care-associated C. difficile infection; for every 10% increase in the proportion of NAP1 strains, the rate of health care-associated C. difficile infection increased by 3.3% (95% CI 1.7%-4.9%).

INTERPRETATION

Rates of health care-associated C. difficile infection have decreased across Canada. In nonepidemic settings, NAP4 has emerged as a common strain type, but NAP1, although decreasing, continues to be the predominant circulating strain and remains significantly associated with higher attributable mortality.

Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes

Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool.

Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia

Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT- toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors.

High prevalence of Clostridium difficile in soil, mulch and lawn samples from the grounds of Western Australian hospitals

Despite being considered a major hospital-associated pathogen for many years, Clostridium difficile has been isolated increasingly from people without hospital contact. In this study, we investigated the prevalence of C. difficile in the immediate outdoor environment of several hospitals in Perth, Western Australia, to provide further insight into potential sources of community-acquired C. difficile infection. Over 6 months, a total of 159 samples consisting of soil, mulch, lawn and sand were collected from outdoor surroundings of four different old (age>50 years) and new (age<10 years) hospitals. Samples were cultured in a C. difficile selective enrichment broth. Toxin gene profiling using PCR, and PCR ribotyping, was performed on all C. difficile recovered. C. difficile was isolated from 96 of the 159 samples (60.4%). Of the 112 isolates, 33 (29.5%) were toxigenic and 49 (43.8%) were identified as novel strains. Ribotypes (RTs) 014/020 (14.3%) and 010 (13.4%) constituted the highest proportion of isolates. Interestingly, RT 017, a strain endemic to the Asia-Pacific region (but not Australia), was found in a newly laid lawn. This study adds to existing knowledge of potential sources of C. difficile in Western Australia. More research is required to determine the route of transmission of C. difficile from community sources into the hospital.

Genomic Delineation of Zoonotic Origins of Clostridium difficile

Clostridium difficile is toxin-producing antimicrobial resistant (AMR) enteropathogen historically associated with diarrhea and pseudomembranous colitis in hospitalized patients. In recent years, there have been dramatic increases in the incidence and severity of C. difficile infection (CDI), and associated morbidity and mortality, in both healthcare and community settings. C. difficile is an ancient and diverse species that displays a sympatric lifestyle, establishing itself in a range of ecological niches external to the healthcare system. These sources/reservoirs include food, water, soil, and over a dozen animal species, in particular, livestock such as pigs and cattle. In a manner analogous to human infection, excessive antimicrobial exposure, particularly to cephalosporins, is driving the expansion of C. difficile in livestock populations worldwide. Subsequent spore contamination of meat, vegetables grown in soil containing animal feces, agricultural by-products such as compost and manure, and the environment in general (households, lawns, and public spaces) is contributing to a persistent community source/reservoir of C. difficile and the insidious rise of CDI in the community. The whole-genome sequencing era continues to redefine our view of this complex pathogen. The application of high-resolution microbial genomics in a One Health framework (encompassing clinical, veterinary, and environment derived datasets) is the optimal paradigm for advancing our understanding of CDI in humans and animals. This approach has begun to yield critical insights into the genetic diversity, evolution, AMR, and zoonotic potential of C. difficile. In Europe, North America, and Australia, microevolutionary analysis of the C. difficile core genome shows strains common to humans and animals (livestock or companion animals) do not form distinct populations but share a recent evolutionary history. Moreover, for C. difficile sequence type 11 and PCR ribotypes 078 and 014, major lineages of One Health importance, this approach has substantiated inter-species clonal transmission between animals and humans. These findings indicate either a zoonosis or anthroponosis. Moreover, they challenge the existing paradigm and the long-held misconception that CDI is primarily a healthcare-associated infection. In this article, evolutionary, and zoonotic aspects of CDI are discussed, including the anthropomorphic factors that contribute to the spread of C. difficile from the farm to the community.

Toxin B Variants from Clostridium difficile Strains VPI 10463 and NAP1/027 Share Similar Substrate Profile and Cellular Intoxication Kinetics but Use Different Host Cell Entry Factors

Clostridium difficile induces antibiotic-associated diarrhea due to the release of toxin A (TcdA) and toxin B (TcdB), the latter being its main virulence factor. The epidemic strain NAP1/027 has an increased virulence attributed to different factors. We compared cellular intoxication by TcdB_NAP1 with that by the reference strain VPI 10463 (TcdB_VPI). In a mouse ligated intestinal loop model, TcdB_NAP1 induced higher neutrophil recruitment, cytokine release, and epithelial damage than TcdB_VPI. Both toxins modified the same panel of small GTPases and exhibited similar in vitro autoprocessing kinetics. On the basis of sequence variations in the frizzled-binding domain (FBD), we reasoned that TcdB_VPI and TcdB_NAP1 might have different receptor specificities. To test this possibility, we used a TcdB from a NAP1 variant strain (TcdB_NAP1v) unable to glucosylate RhoA but with the same receptor-binding domains as TcdB_NAP1. Cells were preincubated with TcdB_NAP1v to block cellular receptors, prior to intoxication with either TcdB_VPI or TcdB_NAP1. Preincubation with TcdB_NAP1v blocked RhoA glucosylation by TcdB_NAP1 but not by TcdB_VPI, indicating that the toxins use different host factors for cell entry. This crucial difference might explain the increased biological activity of TcdB_NAP1 in the intestine, representing a contributing factor for the increased virulence of the NAP1/027 strain.

Enterotoxic Clostridia: Clostridioides difficile Infections

Clostridioides difficile is a Gram-positive, anaerobic, spore forming pathogen of both humans and animals and is the most common identifiable infectious agent of nosocomial antibiotic-associated diarrhea. Infection can occur following the ingestion and germination of spores, often concurrently with a disruption to the gastrointestinal microbiota, with the resulting disease presenting as a spectrum, ranging from mild and self-limiting diarrhea to severe diarrhea that may progress to life-threating syndromes that include toxic megacolon and pseudomembranous colitis. Disease is induced through the activity of the C. difficile toxins TcdA and TcdB, both of which disrupt the Rho family of GTPases in host cells, causing cell rounding and death and leading to fluid loss and diarrhea. These toxins, despite their functional and structural similarity, do not contribute to disease equally. C. difficile infection (CDI) is made more complex by a high level of strain diversity and the emergence of epidemic strains, including ribotype 027-strains which induce more severe disease in patients. With the changing epidemiology of CDI, our understanding of C. difficile disease, diagnosis, and pathogenesis continues to evolve. This article provides an overview of the current diagnostic tests available for CDI, strain typing, the major toxins C. difficile produces and their mode of action, the host immune response to each toxin and during infection, animal models of disease, and the current treatment and prevention strategies for CDI.

Genomics of the Pathogenic Clostridia

Whole-genome sequences are now available for all the clinically important clostridia and many of the lesser or opportunistically pathogenic clostridia. The complex clade structures of C. difficile, C. perfringens, and the species that produce botulinum toxins have been delineated by whole-genome sequence analysis. The true clostridia of cluster I show relatively low levels of gross genomic rearrangements within species, in contrast to the species of cluster XI, notably C. difficile, which have been found to have very plastic genomes with significant levels of chromosomal rearrangement. Throughout the clostridial phylotypes, a large proportion of the strain diversity is driven by the acquisition and loss of mobile elements, including phages, plasmids, insertion sequences, and transposons. Genomic analysis has been used to investigate the diversity and spread of C. difficile within hospital settings, the zoonotic transfer of isolates, and the emergence, origins, and geographic spread of epidemic ribotypes. In C. perfringens the clades defined by chromosomal sequence analysis show no indications of clustering based on host species or geographical location. Whole-genome sequence analysis helps to define the different survival and pathogenesis strategies that the clostridia use. Some, such as C. botulinum, produce toxins which rapidly act to kill the host, whereas others, such as C. perfringens and C. difficile, produce less lethal toxins which can damage tissue but do not rapidly kill the host. The genomes provide a resource that can be mined to identify potential vaccine antigens and targets for other forms of therapeutic intervention.

Evolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance

Historically, Clostridioides difficile (Clostridium difficile) has been associated with life-threatening diarrhea in hospitalized patients. Increasing rates of C. difficile infection (CDI) in the community suggest exposure to C. difficile reservoirs outside the hospital, including animals, the environment, or food. C. difficile sequence type 11 (ST11) is known to infect/colonize livestock worldwide and comprises multiple ribotypes, many of which cause disease in humans, suggesting CDI may be a zoonosis. Using high-resolution genomics, we investigated the evolution and zoonotic potential of ST11 and a new closely related ST258 lineage sourced from diverse origins. We found multiple intra- and interspecies clonal transmission events in all ribotype sublineages. Clones were spread across multiple continents, often without any health care association, indicative of zoonotic/anthroponotic long-range dissemination in the community. ST11 possesses a massive pan-genome and numerous clinically important antimicrobial resistance elements and prophages, which likely contribute to the success of this globally disseminated lineage of One Health importance.

Clostridioides difficile (Clostridium difficile) sequence type 11 (ST11) is well established in production animal populations worldwide and contributes considerably to the global burden of C. difficile infection (CDI) in humans. Increasing evidence of shared ancestry and genetic overlap of PCR ribotype 078 (RT078), the most common ST11 sublineage, between human and animal populations suggests that CDI may be a zoonosis. We performed whole-genome sequencing (WGS) on a collection of 207 ST11 and closely related ST258 isolates of human and veterinary/environmental origin, comprising 16 RTs collected from Australia, Asia, Europe, and North America. Core genome single nucleotide variant (SNV) analysis identified multiple intraspecies and interspecies clonal groups (isolates separated by ≤2 core genome SNVs) in all the major RT sublineages: 078, 126, 127, 033, and 288. Clonal groups comprised isolates spread across different states, countries, and continents, indicative of reciprocal long-range dissemination and possible zoonotic/anthroponotic transmission. Antimicrobial resistance genotypes and phenotypes varied across host species, geographic regions, and RTs and included macrolide/lincosamide resistance (Tn6194 [ermB]), tetracycline resistance (Tn6190 [tetM] and Tn6164 [tet44]), and fluoroquinolone resistance (gyrA/B mutations), as well as numerous aminoglycoside resistance cassettes. The population was defined by a large “open” pan-genome (10,378 genes), a remarkably small core genome of 2,058 genes (only 19.8% of the gene pool), and an accessory genome containing a large and diverse collection of important prophages of the Siphoviridae and Myoviridae. This study provides novel insights into strain relatedness and genetic variability of C. difficile ST11, a lineage of global One Health importance.

Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing

Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

Horizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome of Clostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37 C. difficile isolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly, catD, known to be harbored by Tn4453a/b, was replaced by aac(6′) aph(2′′) in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges between C. difficile and other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified in C. difficile isolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number of C. difficile isolates resistant to all antibiotics tested here suggests the ease with which resistance is acquired in vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.

IMPORTANCE Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

Molecular analysis and genotyping of pathogenicity locus in Clostridioides difficile strains isolated from patients in Tehran hospitals during the years 2007-2010

BACKGROUND & AIMS

Clostridioides difficile (C. difficile) has been identified as the leading cause of antibiotic associated diarrhea (AAD). Co-carriage of an intact pathogenicity locus (PaLoc) with binary toxin genes in C. difficile strains seems to be linked with severe disease outcomes in the infected patients. Epidemiology of C. difficile infection (CDI) in hospital setting and knowledge about their genetic context help us to decrease the morbidity, mortality, and costs associated with Clostridioides difficile infection. In the present study was aimed to characterize genetic diversity of PaLoc among different C. difficile strains isolated from hospitalized patients and carriage of cytolethal distending toxin gene (cdt) in different hospitals.

METHOD

C. difficile strains were isolated from stool samples of inpatients referred to a reference laboratory from different hospitals and also outpatients with diarrhea, during 2008-2011. DNA was extracted from pure culture of the bacterium and PCR was performed for tcdA, tcdB, tcdE, tcdC, tcdD, and cdu2 genes. Carriage of two binary toxin genes cdtA, cdtB was also determined in these strains. To find clonal strains, similarity of genotypes and integrity of PaLoc among the isolates was compared in each hospital.

RESULTS

The intact PaLoc was found most frequently among the isolates in the outpatients (19/51, 37.2%, Group I), while incomplete PaLoc found mostly in patients who were hospitalized in the infectious diseases and internal diagnosis wards. tcdA and tcdB genes were detected in different combinations among the studied strains. These strains showed tcdA⁺B⁺, tcdA⁺B^-, and tcdA^-B⁺ genotypes in a frequency of 76.4% (39/51), 7.8% (4/51), and 17.6% (9/51), respectively. Analysis of gene composition of the PaLoc showed 19 distinct genotypes among the 51 strains. Accordingly, 38 strains were classified mainly into 6 regular groups, while the remaining strains showed heterogeneous patterns. tcdC^-/tcdD^- constituted the most common genotypic group among the strains with partial PaLoc (7/51, 13.7%). A hypertoxigenic genotype, tcdC^-/tcdA⁺/tcdB⁺, was detected in 2 strains (2/51, 3.9%). The intact genotype was also detected in a C. difficile isolate from outpatients. Cdt encoding genes toxins was observed in low numbers of the strains (7/52, 13.5%). All of cdtA⁺B⁺ strains were belonged to PaLoc group 1 (intact genotype). Statistical analyses showed no correlation between particular genotypes and special wards of the hospitals (p value>0.05).

CONCLUSION

Collectively, our results showed diversity of C. difficile strains in most wards of the studied hospitals. Diversity of PaLoc genotypes in the strains that isolated from the same wards proposed endogenous routes of the infection, as common cause of CDI in these patients.

Seasonality and community interventions in a mathematical model of Clostridium difficile transmission

BACKGROUND

Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhoea with peak incidence in late winter or early autumn. Although CDI is commonly associated with hospitals, community transmission is important.

AIM

To explore potential drivers of CDI seasonality and the effect of community-based interventions to reduce transmission.

METHODS

A mechanistic compartmental model of C. difficile transmission in a hospital and surrounding community was used to determine the effect of reducing transmission or antibiotic prescriptions in these settings. The model was extended to allow for seasonal antibiotic prescriptions and seasonal transmission.

FINDINGS

Modelling antibiotic seasonality reproduced the seasonality of CDI, including approximate magnitude (13.9-15.1% above annual mean) and timing of peaks (0.7-1.0 months after peak antibiotics). Halving seasonal excess prescriptions reduced the incidence of CDI by 6-18%. Seasonal transmission produced larger seasonal peaks in the prevalence of community colonization (14.8-22.1% above mean) than seasonal antibiotic prescriptions (0.2-1.7% above mean). Reducing transmission from symptomatic or hospitalized patients had little effect on community-acquired CDI, but reducing transmission in the community by ≥7% or transmission from infants by ≥30% eliminated the pathogen. Reducing antibiotic prescription rates led to approximately proportional reductions in infections, but limited reductions in the prevalence of colonization.

CONCLUSION

Seasonal variation in antibiotic prescription rates can account for the observed magnitude and timing of C. difficile seasonality. Even complete prevention of transmission from hospitalized patients or symptomatic patients cannot eliminate the pathogen, but interventions to reduce transmission from community residents or infants could have a large impact on both hospital- and community-acquired infections.

The first isolation of Clostridium difficile RT078/ST11 from pigs in China

We investigated the molecular characteristics and antimicrobial susceptibility of Clostridium difficile isolated from animals in China. We obtained 538 rectal swabs from pigs, chickens and ducks in 5 provinces during 2015 and 2016. C. difficile isolates were characterized by detection of toxin genes, multilocus sequence typing and ribotyping. And antimicrobial susceptibility testing was performed using the agar dilution method. Out of 538 samples, 44 (8.2%) were C. difficile positive with high prevalence in pigs (n = 31). Among these, 39 (88.6%) were toxigenic including 14 (31.8%) that were A+B+CDT+ and 13 (29.5%) A+B+. The remaining 12 (27.3%) were A-B+. We identified 7 ST types and 6 PCR ribotypes. The most predominant type was ST11/RT078 with toxin profile A+B+CDT+ and all were isolated from piglets with diarrhea. ST109 isolates possessed two different toxigenic profiles (A-B-CDT- and A-B+CDT-) and although it was not the most prevalent sequence type, but it was widely distributed between chickens, ducks and pigs in the 5 provinces. All C. difficile isolates were fully susceptible to vancomycin, metronidazole, fidaxomicin, amoxicillin/clavulanate and meropenem but retained resistance to 4 or 5 of the remaining antibiotics, especially cefotaxime, tetracycline, ciprofloxacin, cefoxitin. The RT078/ST11 isolates were simultaneously resistant to cefotaxime, tetracycline, cefoxitin, ciprofloxacin and imipenem. This is the first report of the molecular epidemiology of C. difficile isolated from food animals in China. We identified the epidemic strain RT078/ST11 as the predominate isolate among the animals we screened in our study.

Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile

Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.

Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea

Clostridioides difficile infection (CDI) is currently one of the most important causes of infectious diarrhea in developed countries and the main cause in healthcare settings. Here, we characterized the gut microbiota from the feces of 57 patients with diarrhea from nosocomial and community-acquired CDI. We performed an ecological analysis by high-throughput sequencing of the V3-V4 region of 16S rRNA amplicons and evaluated the association of the various ecological profiles with CDI risk factors. Among all samples Bacteroidaceae 31.01%, Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6,16%, and Ruminococcaceae 5.64%, were the most abundant families. A reduced abundance of Bacteroides was associated with a poor CDI prognosis, with severe diarrhea and a high incidence of recurrence. This reduction was associated with a weakened host immune system and previous aggressive antibiotherapy. Peptostreptococcaceae family was 1.56% overall and within the family the only identified member was the genus Clostridioides, positively correlated with the presence of Akkermansia that may be predictive of the presence of a CDI. Finally, a relevant aspect that must be considered in clinical practice is the misdiagnosis of CDI, as patients with a stool sample that tests positive for C. difficile are usually diagnosed with CDI and subsequently treated as such. However, co-infection with other pathogenic agents often plays an important role in the development of diarrhea, and must be considered when prescribing antibiotic treatment.

Prevalence, genotype and antimicrobial resistance of Clostridium difficile isolates from healthy pets in Eastern China

BACKGROUND

Clostridium difficile (C. difficile) is a main cause of antibiotic-associated diarrhoea in humans. Several studies have been performed to reveal the prevalence rate of C. difficile in cats and dogs. However, little is known about the epidemiology of C. difficile in healthy pets in China. This study aimed to assess the burden of C. difficile shedding by healthy dogs and cats in China. Furthermore, the genetic diversity and antimicrobial susceptibility patterns of the recovered isolates were determined.

METHODS

A total of 175 faecal samples were collected from 146 healthy dogs and 29 cats. C. difficile strains were isolated and identified from the feces of these pets. The characterized C. difficile strains were typed by multilocus sequence typing (MLST), and the MICs of the isolates were determined against ampicillin, clindamycin, tetracycline, moxifloxacin, chloramphenicol, cefoxitin, metronidazole and vancomycin by the agar dilution method.

RESULTS

Overall, 3 faecal samples (1.7%) were C. difficile culture positive. One sample (0.7%) from a dog was C. difficile culture positive, while two cats (7.0%) yielded positive cultures. The prevalence rate differed significantly between cats and dogs. These isolates were typed into 3 MLST genotypes and were susceptible to chloramphenicol, tetracycline, metronidazole and moxifloxacin and resistant to ampicillin, clindamycin and cefoxitin. Notably, one strain, D141-1, which was resistant to three kinds of antibiotics and carried toxin genes, was recovered in the faeces of a healthy dog.

CONCLUSION

Our results suggest that common pets may be a source of pathogenic C. difficile, indicating that household transmission of C. difficile from pets to humans can not be excluded.

Immune cell counts and signaling in body fluids of cows vaccinated against Clostridium difficile

BACKGROUND

New treatment options are needed to prevent relapses following failed antibiotic therapies of Clostridium difficile infections (CDI) in humans. The concomitant therapy with an anti-C. difficile IgA containing whey protein concentrate can support the sustainable recovery of CDI patients. For 31 weeks, nine dairy cows were continuously vaccinated with several anti-C. difficile vaccines by certain routes of administration to produce anti-C. difficile IgA enriched milk. The study aimed at finding decisive differences between low responder (LR) and high responder (HR) cows (> 8.0 µg ml-1 total milk C. difficile specific IgA) concerning their immune response to vaccination on cellular and molecular biological levels.

RESULTS

The results of total and differential cell counting (DCC) in blood and milk and the outcomes of the gene expression analysis of selected immune factors were assessed relating to the usage of two vaccine batches for injection (MucoCD-I batch A and B), marking two immunization (IM) periods, and compared to a control group (Ctr). The MucoCD-I batch A caused short-term leukopenia followed by leukocytosis in the blood of LR and HR. The total somatic cell counts in milk were not altered by the treatment. The DCC revealed that the leukocytes of the treated groups were partly impaired by the treatment. The gene expression analysis exposed cumulative and sustainable differences (p < 0.05) between LR and HR for the genes encoding for lactoferrin, CXCL8, IL1β, IL2, IL6, IL12β, IFNγ, CD4 and CD163. The regulation of the epithelial IgA cell receptor PIGR was not impaired by the IM. In contrast to the vaccination with MucoCD-I batch A, the second IM period with MucoCD-I batch B resulted in mitigation and synchronization of the treated groups' immune responses.

CONCLUSIONS

The inversely regulated cytokines in the blood and milk cells of the treated groups led to a variously directed, local T cell response resulting in their different production intensities of C. difficile specific IgA in milk.

A series of three cases of severe Clostridium difficile infection in Australia associated with a binary toxin producing clade 2 ribotype 251 strain

Three patients with severe Clostridium difficile infection (CDI) caused by an unusual strain of C. difficile, PCR ribotype (RT) 251, were identified in New South Wales, Australia. All cases presented with severe diarrhoea, two had multiple recurrences and one died following a colectomy. C. difficile RT251 strains were isolated by toxigenic culture. Genetic characterisation was performed using techniques including toxin gene profiling, PCR ribotyping, whole genome sequencing (WGS), in-silico multi-locus-sequence-typing (MLST) and core-genome single nucleotide variant (SNV) analyses. Antimicrobial susceptibility was determined using an agar incorporation method. In vitro toxin production was confirmed by Vero cell cytotoxicity assay and pathogenicity was assessed in a murine model of CDI. All RT251 isolates contained toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB) genes. Core-genome analyses revealed the RT251 strains were clonal, with 0-5 SNVs between isolates. WGS and MLST clustered RT251 in the same evolutionary clade (clade 2) as RT027. Despite comparatively lower levels of in vitro toxin production, in the murine model RT251 infection resembled RT027 infection. Mice showed marked weight loss, severe disease within 48 h post-infection and death. All isolates were susceptible to metronidazole and vancomycin. Our observations suggest C. difficile RT251 causes severe disease and emphasise the importance of ongoing surveillance for new and emerging strains of C. difficile with enhanced virulence.

Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS

OBJECTIVES

Clostridioides difficile infection (CDI) has become the main cause of nosocomial infective diarrhoea. To survey and control the spread of different C. difficile strains, there is a need for suitable rapid tests. The aim of this study was to identify peptide/protein markers for the rapid recognition of C. difficile strains by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS).

METHODS

We analysed 44 well-characterized strains, belonging to eight different multi-locus sequence types (MLST), using ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS. The amino acid sequence of two peptide markers specific for MLST-1 and MLST-11 strains was elucidated by MALDI-TOF-MS/MS. The investigation of 2689 C. difficile genomes allowed the determination of the sensitivity and specificity of these markers. C18-solid-phased extraction was used to enrich the MLST-1 marker.

RESULTS

Two peptide markers (m/z 4927.81 and m/z 5001.84) were identified and characterized for MLST-1 and MLST-11 strains, respectively. The MLST-1 marker was found in 786 genomes of which three did not belong to MLST-1. The MLST-11 marker was found in 319 genomes, of which 14 did not belong to MLST-11. Importantly, all MLST-1 and MLST-11 genomes were positive for their respective marker. Furthermore, a peptide marker (m/z 5015.86) specific for MLST-15 was found in 59 genomes. We translated our findings into a fast and simple method that allowed the unambiguous identification of the MLST-1 marker on a MALDI-TOF-MS platform.

CONCLUSIONS

MALDI-FTICR MS-based peptide profiling resulted in the identification of peptide markers for C. difficile MLST-1 and MLST-11.

Effect of natural products on the production and activity of Clostridium difficile toxins in vitro

Clostridium difficile infection is a toxin-mediated disease of the colon. C. difficile virulence is primarily attributed to the production of toxin A and toxin B; thus this study was aimed to investigate the effect of a range of natural products on the production and activity of C. difficile toxins in vitro. Twenty-two natural products were investigated against four C. difficile strains. The activity of products against toxins was determined using Vero and HT-29 cells cytotoxicity and neutral red uptake assays. The indirect effect of products on toxin-mediated cytotoxicity was determined using the same cell lines. The effect of seven products on toxin production by C. difficile was determined using ELISA. Zingerone (0.3 mg/ml) protected both cell lines from C. difficile cytopathic effects, confirmed by the neutral red uptake assay (P < 0.05). Three Leptospermum honeys (4% w/v), fresh onion bulb extract (12.5% v/v) and trans-cinnamaldehyde (0.005% v/v) all reduced toxin production and activity significantly (P ≤ 0.023). Garlic clove powder (4.7 mg/ml) only reduced toxin activity (P ≤ 0.047). Overall, several natural products had activity against C. difficile toxins in vitro encouraging further investigation against C. difficile toxins in vivo.

Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

Clostridiodes difficile strains from the NAP_CR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAP_CR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAP_CR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAP_CR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAP_CR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAP_CR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAP_CR1/ST54 isolates showed 1 recombination block (3,301–8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAP_CR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAP_CR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAP_CR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAP_CR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.

Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements

The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.

Clostridioides difficile in the environment, food, animals and humans in southern Italy: Occurrence and genetic relatedness

One hundred and thirty-eight C. difficile isolates from different sources (66 from the environment, 36 from animals, 9 from food and 27 from humans) were ribotyped by capillary electrophoresis PCR ribotyping (CE-PCR). A multilocus variable tandem repeat analysis (MLVA) was carried out on a sample subset. The most frequently isolated PCR ribotypes were 126 (15.9%), 078 (14.5%), 011/018 (11.6%), 014/020/077 (10.1%), and 010 (2.8%). In particular, strains of PCR ribotype 011/018 were isolated from human, raw milk and environmental samples. The hypervirulent PCR ribotype 027 was isolated from two human samples. The majority of the strains were toxigenic (34.1% showed the toxigenic profile A⁺B⁺CDT⁺ and 38.9% the profile A⁺B⁺CDT^-). MLVA allowed to identify 4 clonal complexes of genetically related isolates: complex n. 1 grouped together human, environmental and food strains, whereas complex n. 3 included human and environmental isolates. The use of MLVA gave further evidence to the possible role of environment, animals and food as routes of transmission of C. difficile infections to human.

Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study

Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A⁺/B⁺ ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A⁺/B⁺ ribotype SLO160 and toxin A^-/B⁺ ribotype 017. With 42.9–73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed.

Clostridium difficile colitis and zoonotic origins-a narrative review

Clostridium difficile is a major cause of hospital-associated diarrhoea, and in severe cases leads to pseudomembranous colitis and toxic megacolon. The frequency of C. difficile infection (CDI) has increased in recent decades, with 453 000 cases identified in 2011 in the USA. This is related to antibiotic-selection pressure, disruption of normal host intestinal microbiota and emergence of antibiotic-resistant C. difficile strains. The burden of community-acquired CDI has been increasingly appreciated, with disease identified in patients previously considered low-risk, such as young women or patients with no prior antibiotic exposure. C. difficile has been identified in livestock animals, meat products, seafood and salads. It has been postulated that the pool of C. difficile in the agricultural industry may contribute to human CDI. There is widespread environmental dispersal of C. difficile spores. Domestic households, turf lawns and public spaces are extensively contaminated, providing a potential reservoir for community-acquired CDI. In Australia, this is particularly associated with porcine-derived C. difficile UK PCR ribotype 014/020. In this article, the epidemiological differences between hospital- and community-acquired CDI are discussed, including some emerging evidence for community-acquired CDI being a possible zoonosis.

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile

Clostridium difficile, recently renamed Clostridioides difficile, is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping (n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.

Antimicrobial susceptibility of Clostridium difficile isolated from food and environmental sources in Western Australia

We recently reported a high prevalence of Clostridium difficile in retail vegetables, compost and lawn in Western Australia. The objective of this study was to investigate the antimicrobial susceptibility of previously isolated food and environmental C. difficile isolates from Western Australia. A total of 274 C. difficile isolates from vegetables, compost and lawn were tested for susceptibility to a panel of 10 antimicrobial agents (fidaxomicin, vancomycin, metronidazole, rifaximin, clindamycin, erythromycin, amoxicillin/clavulanic acid, moxifloxacin, meropenem and tetracycline) using the agar incorporation method. Fidaxomicin was the most potent agent (MIC₅₀/MIC₉₀, 0.06/0.12 mg/L). Resistance to fidaxomicin and metronidazole was not detected and resistance to vancomycin (0.7%) and moxifloxacin (0.7%) was low. However, 103 isolates (37.6%) showed resistance to at least one agent, and multidrug resistance was observed in 3.9% of the resistant isolates (4/103), all of which came from compost. A significantly greater proportion of compost isolates were resistant to clindamycin, erythromycin and tetracycline compared with food and/or lawn isolates. Clostridium difficile ribotype (RT) 014/020 showed greater clindamycin resistance than other less common RTs (P = 0.008, χ²). Contaminated vegetables, compost and lawn could be playing an intermediary role in the transmission of C. difficile from animals to humans. Environmental strains of C. difficile could also function as a reservoir for antimicrobial resistance genes of clinical relevance. This study provides a baseline for future surveillance of antimicrobial resistance in environmental C. difficile isolates in Australia.

Antibiotic susceptibility and resistance profiles of Romanian Clostridioides difficile isolates

This study investigated the antibiotic susceptibility patterns and genetic resistance markers of 35 C. difficile strains isolated from patients with C. difficile infection. Vancomycin, metronidazole, tigecycline, teicoplanin, rifampicin, moxifloxacin, cefotaxime, tetracycline, erythromycin, clindamycin, chloramphenicol, linezolid and imipenem MICs were determined for toxigenic strains belonging to PCR ribotypes (PR) 012 (2), 014 (4), 017 (3), 018 (2), 027 (17), 046 (2), 087 (3) and 115 (2). Results showed vancomycin, metronidazole, tigecycline and teicoplanin to be active against all isolates. High resistance rates were noticed against cefotaxime (n = 35), clindamycin (n = 33), imipenem (n = 31), moxifloxacin (n = 25), erythromycin (n = 25) and rifampicin (n = 22). Linezolid-resistance was found in three isolates (PR 017/2, PR 012/1), showing complex resistance (7-9 antibiotics). PR 012, 017, 018, 027 and 046 isolates (n = 26) were resistant to 5-9 antibiotics. Twelve resistance profiles (2-9 antibiotics) were detected. Rifampicin-moxifloxacin-cefotaxime-erythromycin-clindamycin-imipenem-resistance was predominant, being expressed by 18 strains (PR 027/17, PR 018/1). PCR results suggested tetracycline-resistance to be induced by the gene tetM. Three tetM-positive isolates (PRs 012, 046), were also tndX-positive, suggesting the presence of a Tn5397-like element. Only two MLSB-resistant strains (PR 012) had the ermB gene and chloramphenicol-resistance determinant catD was not detected, leaving room for further investigating resistance mechanisms. Multidrug resistance could be attributed to most analysed strains, underlining, once more, the impact of wide-spectrum antimicrobial over prescription, still a tendency in our country, on transmission of antimicrobial resistance and emergence of epidemic C. difficile strains generating outbreaks.

Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production

We report the frequent, convergent loss of two genes encoding the substrate-binding protein and the ATP-binding protein of an ATP-binding cassette (ABC) transporter from the genomes of unrelated Clostridioides difficile strains. This specific genomic deletion was strongly associated with the reduced uptake of tyrosine and phenylalanine and production of derived Stickland fermentation products, including p-cresol, suggesting that the affected ABC transporter had been responsible for the import of aromatic amino acids. In contrast, the transporter gene loss did not measurably affect bacterial growth or production of enterotoxins. Phylogenomic analysis of publically available genome sequences indicated that this transporter gene deletion had occurred multiple times in diverse clonal lineages of C. difficile, with a particularly high prevalence in ribotype 027 isolates, where 48 of 195 genomes (25%) were affected. The transporter gene deletion likely was facilitated by the repetitive structure of its genomic location. While at least some of the observed transporter gene deletions are likely to have occurred during the natural life cycle of C. difficile, we also provide evidence for the emergence of this mutation during long-term laboratory cultivation of reference strain R20291.

Characteristics and Immunological Roles of Surface Layer Proteins in Clostridium difficile

Clostridium difficile is a major causative agent of antibiotic-associated diarrhea and has become the most common pathogen of healthcare-associated infection worldwide. The pathogenesis of C. difficile infection (CDI) is mediated by many factors such as colonization involving attachment to host intestinal epithelial cells, sporulation, germination, and toxin production. Bacterial cell surface components are crucial for the interaction between the bacterium and host cells. C. difficile has two distinct surface layer proteins (SLPs): a conserved high-molecular-weight SLP and a highly variable low-molecular-weight SLP. Recent studies have shown that C. difficile SLPs play roles not only in growth and survival, but also in adhesion to host epithelial cells and induction of cytokine production. Sequence typing of the variable region of the slpA gene, which encodes SLPs, is one of the methods currently used for typing C. difficile. SLPs have received much attention in recent years as vaccine candidates and new therapeutic agents in the treatment of C. difficile-associated diseases. Gaining mechanistic insights into the molecular functions of C. difficile SLPs will help advance our understanding of CDI pathogenesis and the development of vaccines and new therapeutic approaches. In this review, we summarize the characteristics and immunological roles of SLPs in C. difficile.

Molecular Characterization of Clostridium difficile Isolates in China From 2010 to 2015

Clostridium difficile infection (CDI) has become a worldwide public health problem causing high mortality and a large disease burden. Molecular typing and analysis is important for surveillance and infection control of CDI. However, molecular characterization of C. difficile across China is extremely rare. Here, we report on the toxin profiles, molecular subtyping with multilocus sequence typing (MLST) and PCR ribotyping, and epidemiological characteristics of 199 C. difficile isolates collected between 2010 through 2015 from 13 participating centers across China. We identified 35 STs and 27 ribotypes (RTs) among the 199 C. difficile isolates: ST35 (15.58%), ST3 (15.08%), ST37 (12.06%), and RT017 (14.07%), RT001 (12.06%), RT012 (11.56%) are the most prevalent. One isolate with ST1 and 8 isolates with ST 11 were identified. We identified a new ST in this study, denoted ST332. The toxin profile tcdA⁺tcdB⁺tcdC⁺tcdR⁺tcdE⁺CDT^- (65.83%) was the predominant profile. Furthermore, 11 isolates with positive binary toxin genes were discovered. According to the PCR ribotyping, one isolate with RT 027, and 6 isolates with RT 078 were confirmed. The epidemiological characteristics of C. difficile in China shows geographical differences, and both the toxin profile and molecular types exhibit great diversity across the different areas.

Molecular epidemiology of Clostridium difficile in two tertiary care hospitals in Shandong Province, China

Purpose

The incidence and severity of Clostridium difficile infection (CDI) have markedly increased over the past decade. However, there is very limited epidemiological data on CDI in China so far, specifically no data in Shandong Province. The aim of this study was to evaluate diagnostic algorithm for CDI and to gain data on molecular epidemiology of CDI in the Shandong Province of China.

Materials and methods

Nonrepetitive unformed fecal specimens (n=504) were investigated by the glutamate dehydrogenase (GDH), C. difficile toxin A&B (CDAB) tests and toxigenic culture. Furthermore, 85 isolates were characterized by toxin gene detection, multilocus sequence typing, ribotyping and antimicrobial susceptibility testing.

Results

The algorithm of combining GDH and CDAB tests could define diagnosis of 54.2% CDI cases and excluded 90% of non-CDI. Further adding the toxigenic culture to the algorithm enhanced the detection sensitivity to 100%. Toxigenic strains comprised 84.7% of isolates, including A+B+CDT− (71.8%, 61/85), A−B+CDT− (11.8%, 10/85) and A+B+CDT+ (1.2%, 1/85) isolates. RT046/ST35 (13.9%, 10/72), RT014/ST2 (12.5%, 9/72) and RT017/ST37 (12.5%, 9/72) were the more common genotypes among toxigenic C. difficile strains. The clinical severity score of A−B+CDT− toxin genes genotype (3.50±0.85) was significantly higher than the A+B+CDT− type (2.59±0.93) (P<0.05). RT046/ST35 isolates were highly prevalent and had high clinical severity scores (3.80±0.92). Variations in resistance from different sequence types (STs) were observed. Toxigenic strains showed higher resistance rates to erythromycin, clindamycin and ciprofloxacin compared to nontoxigenic strains (P<0.05).

Conclusion

The epidemiology of C. difficile in Shandong Province differed from other regions in China. Comprehensive optimized diagnosis strategy and continuous surveillance should be established and applied in order to curb the spread of toxigenic C. difficile strains, especially for hospitalized patients.

Understanding Clostridium difficile Colonization

Clostridium difficile is the main causative agent of antibiotic-associated and health care-associated infective diarrhea. Recently, there has been growing interest in alternative sources of C. difficile other than patients with Clostridium difficile infection (CDI) and the hospital environment. Notably, the role of C. difficile-colonized patients as a possible source of transmission has received attention. In this review, we present a comprehensive overview of the current understanding of C. difficile colonization. Findings from gut microbiota studies yield more insights into determinants that are important for acquiring or resisting colonization and progression to CDI. In discussions on the prevalence of C. difficile colonization among populations and its associated risk factors, colonized patients at hospital admission merit more attention, as findings from the literature have pointed to their role in both health care-associated transmission of C. difficile and a higher risk of progression to CDI once admitted. C. difficile colonization among patients at admission may have clinical implications, although further research is needed to identify if interventions are beneficial for preventing transmission or overcoming progression to CDI.

A retrospective study of community-acquired Clostridium difficile infection in southwest China

To identify the prevalence and characteristics of community-acquired Clostridium difficile infection (CA-CDI) in southwest China, we conducted a cross-sectional study. 978 diarrhea patients were enrolled and stool specimens’ DNA was screened for virulence genes. Bacterial culture was performed and isolates were characterized by PCR ribotyping and multilocus sequence typing. Toxin genes tcdA and/or tcdB were found in 138/978 (14.11%) cases for fecal samples. A total of 55 C. difficile strains were isolated (5.62%). The positive rate of toxin genes and isolation results had no statistical significance between children and adults groups. However, some clinical features, such as fecal property, diarrhea times before hospital treatment shown difference between two groups. The watery stool was more likely found in children, while the blood stool for adults; most of children cases diarrhea ≤3 times before hospital treatment, and adults diarrhea >3 times. Independent risk factor associated with CA-CDI was patients with fever. ST35/RT046 (18.18%), ST54/RT012 (14.55%), ST3/RT001 (14.55%) and ST3/RT009 (12.73%) were the most distributed genotype profiles. ST35/RT046, ST3/RT001 and ST3/RT009 were the commonly found in children patients but ST54/RT012 for adults. The prevalence of CA-CDI in Yunnan province was relatively high, and isolates displayed heterogeneity between children and adults groups.

Aliyu S, F. Hadjirin N, A. Holmes M, Török E, M. Brown N, Parkhill J, Peacock S. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages

There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.